2-95950754-A-T

Variant names:

• chr2-95950754-A-T
• NM_001393982.1:c.1290T>A

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.1290T>A​(p.Val430Val) 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: 140)
• Consequence: ANKRD36C NM_001393982.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.714

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=-1.07).
• BP6: Variant 2-95950754-A-T is Benign according to our data. Variant chr2-95950754-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 3389383.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.714 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36C	NM_001393982.1	c.1290T>A	p.Val430Val	synonymous_variant	Exon 16 of 88	ENST00000295246.7	NP_001380911.1
ANKRD36C	NM_001310154.3	c.1290T>A	p.Val430Val	synonymous_variant	Exon 16 of 89		NP_001297083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD36C	ENST00000295246.7	c.1290T>A	p.Val430Val	synonymous_variant	Exon 16 of 88	5	NM_001393982.1	ENSP00000295246.7
ANKRD36C	ENST00000456556.5	c.1290T>A	p.Val430Val	synonymous_variant	Exon 16 of 67	5		ENSP00000403302.1
ANKRD36C	ENST00000528268.5	n.1290T>A		non_coding_transcript_exon_variant	Exon 16 of 27	2		ENSP00000431824.1

Frequencies

GnomAD3 genomes Cov.: 140

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 140

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Oct 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ANKRD36C: PM2:Supporting, BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.6
DANN	Benign	0.28
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-96616502;