chr17-79047677-C-T

Variant names:

• chr17-79047677-C-T
• rs34874100
• NM_030968.5:c.435C>T

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_030968.5(C1QTNF1):​c.435C>T​(p.Tyr145Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00515 in 1,613,954 control chromosomes in the GnomAD database, including 386 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.027 (208 hom., cov: 32)
  • Exomes 𝑓: 0.0028 (178 hom.)
• Consequence: C1QTNF1 NM_030968.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.362
• Publications: 2 publications found

Genes affected

C1QTNF1 (HGNC:14324): (C1q and TNF related 1) Enables collagen binding activity. Involved in several processes, including negative regulation of platelet aggregation; positive regulation of aldosterone secretion; and positive regulation of cytosolic calcium ion concentration. Located in extracellular space. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BP6: Variant 17-79047677-C-T is Benign according to our data. Variant chr17-79047677-C-T is described in ClinVar as Benign. ClinVar VariationId is 781391.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.362 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0923 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030968.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF1	NM_030968.5	MANE Select	c.435C>T	p.Tyr145Tyr	synonymous	Exon 4 of 4	NP_112230.1	Q9BXJ1-1
	C1QTNF1	NM_153372.3		c.435C>T	p.Tyr145Tyr	synonymous	Exon 4 of 4	NP_699203.1	Q9BXJ1-1
	C1QTNF1	NM_198593.4		c.435C>T	p.Tyr145Tyr	synonymous	Exon 4 of 4	NP_940995.1	Q9BXJ1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF1	ENST00000579760.6	TSL:1 MANE Select	c.435C>T	p.Tyr145Tyr	synonymous	Exon 4 of 4	ENSP00000463922.1	Q9BXJ1-1
	C1QTNF1	ENST00000580474.1	TSL:1	c.435C>T	p.Tyr145Tyr	synonymous	Exon 3 of 3	ENSP00000463108.1	Q9BXJ1-1
	C1QTNF1	ENST00000581774.5	TSL:1	c.435C>T	p.Tyr145Tyr	synonymous	Exon 4 of 4	ENSP00000462481.2	Q9BXJ1-1

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4133 AN: 152144 Hom.: 204 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00981

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000338

Gnomad OTH AF: 0.0182

GnomAD2 exomes AF: 0.00711 AC: 1787 AN: 251176 AF XY: 0.00510

Gnomad AFR exome AF: 0.0961

Gnomad AMR exome AF: 0.00509

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000273

Gnomad OTH exome AF: 0.00229

GnomAD4 exome AF: 0.00285 AC: 4162 AN: 1461692 Hom.: 178 Cov.: 32 AF XY: 0.00252 AC XY: 1830 AN XY: 727144

African (AFR) AF: 0.0977 AC: 3272 AN: 33480

American (AMR) AF: 0.00541 AC: 242 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26114

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.000116 AC: 10 AN: 86248

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53384

Middle Eastern (MID) AF: 0.00434 AC: 25 AN: 5766

European-Non Finnish (NFE) AF: 0.000215 AC: 239 AN: 1111894

Other (OTH) AF: 0.00619 AC: 374 AN: 60394

GnomAD4 genome AF: 0.0272 AC: 4149 AN: 152262 Hom.: 208 Cov.: 32 AF XY: 0.0259 AC XY: 1926 AN XY: 74456

African (AFR) AF: 0.0948 AC: 3936 AN: 41528

American (AMR) AF: 0.00980 AC: 150 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000338 AC: 23 AN: 68016

Other (OTH) AF: 0.0180 AC: 38 AN: 2114

Alfa AF: 0.0118 Hom.: 71

Bravo AF: 0.0313

Asia WGS AF: 0.00837 AC: 30 AN: 3478

EpiCase AF: 0.000545

EpiControl AF: 0.000356

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	9.3
DANN	Benign	0.71
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs34874100; hg19: chr17-77043759; COSMIC: COSV59263639;