chr2-95853727-T-C

Variant names:

• chr2-95853727-T-C
• rs201755982
• NM_001393982.1:c.6153A>G

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001393982.1(ANKRD36C):​c.6153A>G​(p.Leu2051Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,588,308 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0010 (0 hom., cov: 30)
  • Exomes 𝑓: 0.0012 (1 hom.)
• Consequence: ANKRD36C NM_001393982.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.845
• Publications: 0 publications found

Genes affected

ANKRD36C (HGNC:32946): (ankyrin repeat domain 36C)

ENSG00000290897 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 2-95853727-T-C is Benign according to our data. Variant chr2-95853727-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2651122.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.845 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393982.1. 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
	ANKRD36C	NM_001393982.1	MANE Select	c.6153A>G	p.Leu2051Leu	synonymous	Exon 84 of 88	NP_001380911.1	A0A8J8YUB5
	ANKRD36C	NM_001310154.3		c.6228A>G	p.Leu2076Leu	synonymous	Exon 85 of 89	NP_001297083.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD36C	ENST00000295246.7	TSL:5 MANE Select	c.6153A>G	p.Leu2051Leu	synonymous	Exon 84 of 88	ENSP00000295246.7	A0A8J8YUB5
	ANKRD36C	ENST00000612359.5	TSL:1	c.246A>G	p.Leu82Leu	synonymous	Exon 2 of 6	ENSP00000485004.2
	ANKRD36C	ENST00000488721.5	TSL:1	n.1303A>G		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.00101 AC: 154 AN: 152080 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.000290

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000656

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00188

Gnomad OTH AF: 0.000957

GnomAD2 exomes AF: 0.000808 AC: 143 AN: 176890 AF XY: 0.000764

Gnomad AFR exome AF: 0.000270

Gnomad AMR exome AF: 0.000648

Gnomad ASJ exome AF: 0.000225

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000567

Gnomad NFE exome AF: 0.00160

Gnomad OTH exome AF: 0.000419

GnomAD4 exome AF: 0.00124 AC: 1780 AN: 1436110 Hom.: 1 Cov.: 30 AF XY: 0.00125 AC XY: 888 AN XY: 711942

African (AFR) AF: 0.0000906 AC: 3 AN: 33112

American (AMR) AF: 0.000578 AC: 24 AN: 41498

Ashkenazi Jewish (ASJ) AF: 0.0000777 AC: 2 AN: 25724

East Asian (EAS) AF: 0.00 AC: 0 AN: 39008

South Asian (SAS) AF: 0.000217 AC: 18 AN: 82786

European-Finnish (FIN) AF: 0.0000577 AC: 3 AN: 52032

Middle Eastern (MID) AF: 0.000244 AC: 1 AN: 4106

European-Non Finnish (NFE) AF: 0.00152 AC: 1669 AN: 1098508

Other (OTH) AF: 0.00101 AC: 60 AN: 59336

GnomAD4 genome AF: 0.00101 AC: 154 AN: 152198 Hom.: 0 Cov.: 30 AF XY: 0.00102 AC XY: 76 AN XY: 74424

African (AFR) AF: 0.000289 AC: 12 AN: 41536

American (AMR) AF: 0.000655 AC: 10 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

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

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.00188 AC: 128 AN: 67992

Other (OTH) AF: 0.000947 AC: 2 AN: 2112

Alfa AF: 0.00154 Hom.: 0

Bravo AF: 0.00113

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.86
DANN	Benign	0.36
PhyloP100		0.84
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs201755982; hg19: chr2-96519475;