chr5-1297373-C-T

Variant names:

• chr5-1297373-C-T
• rs2736108

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.244 in 152,164 control chromosomes in the GnomAD database, including 5,188 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (5188 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.679
• Publications: 78 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 5-1297373-C-T is Benign according to our data. Variant chr5-1297373-C-T is described in ClinVar as Benign. ClinVar VariationId is 225785.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37151 AN: 152046 Hom.: 5179 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.274

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.244 AC: 37171 AN: 152164 Hom.: 5188 Cov.: 33 AF XY: 0.244 AC XY: 18187 AN XY: 74386

African (AFR) AF: 0.123 AC: 5113 AN: 41522

American (AMR) AF: 0.228 AC: 3481 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1220 AN: 3472

East Asian (EAS) AF: 0.290 AC: 1501 AN: 5178

South Asian (SAS) AF: 0.516 AC: 2482 AN: 4814

European-Finnish (FIN) AF: 0.214 AC: 2272 AN: 10598

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20079 AN: 67970

Other (OTH) AF: 0.283 AC: 598 AN: 2112

Alfa AF: 0.278 Hom.: 12894

Bravo AF: 0.236

Asia WGS AF: 0.412 AC: 1430 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.33
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2736108; hg19: chr5-1297488;