chr2-95855848-C-G

Position:

• chr2-95855848-C-G

Variant summary

Our verdict is Likely benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -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 id is 2651127.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.381 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD36C	NM_001393982.1	c.5436G>C	p.Leu1812Leu	synonymous_variant	83/88	ENST00000295246.7	NP_001380911.1
ANKRD36C	NM_001310154.3	c.5511G>C	p.Leu1837Leu	synonymous_variant	84/89		NP_001297083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD36C	ENST00000295246.7	c.5436G>C	p.Leu1812Leu	synonymous_variant	83/88	5	NM_001393982.1	ENSP00000295246.7
ANKRD36C	ENST00000488721.5	n.586G>C		non_coding_transcript_exon_variant	3/4	1
ANKRD36C	ENST00000456556.5	c.4413G>C	p.Leu1471Leu	synonymous_variant	63/67	5		ENSP00000403302.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2023

ANKRD36C: PM2:Supporting, BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.45
DANN	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs151242024; hg19: chr2-96521596; COSMIC: COSV69432708; COSMIC: COSV69432708;