2-95855848-C-G

Variant names:

• chr2-95855848-C-G
• rs151242024
• NM_001393982.1:c.5436G>C

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_001393982.1(ANKRD36C):​c.5436G>C​(p.Leu1812Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ANKRD36C NM_001393982.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.381
• Publications: 0 publications found

Genes affected

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

ENSG00000290897 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BP6: Variant 2-95855848-C-G is Benign according to our data. Variant chr2-95855848-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2651127.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.381 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.5436G>C	p.Leu1812Leu	synonymous	Exon 83 of 88	NP_001380911.1	A0A8J8YUB5
	ANKRD36C	NM_001310154.3		c.5511G>C	p.Leu1837Leu	synonymous	Exon 84 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.5436G>C	p.Leu1812Leu	synonymous	Exon 83 of 88	ENSP00000295246.7	A0A8J8YUB5
	ANKRD36C	ENST00000488721.5	TSL:1	n.586G>C		non_coding_transcript_exon	Exon 3 of 4
	ANKRD36C	ENST00000456556.5	TSL:5	c.4413G>C	p.Leu1471Leu	synonymous	Exon 63 of 67	ENSP00000403302.1	Q5JPF3-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

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	-0.65
CADD	Benign	0.45
DANN	Benign	0.40
PhyloP100		0.38
PromoterAI		-0.0054	Neutral
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: rs151242024; hg19: chr2-96521596; COSMIC: COSV69432708; COSMIC: COSV69432708;