2-95902947-G-C

Variant names:

• chr2-95902947-G-C
• NM_001393982.1:c.3204C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001393982.1(ANKRD36C):​c.3204C>G​(p.Asp1068Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000139 in 1,437,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. D1068D) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: ANKRD36C NM_001393982.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.88

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36C	NM_001393982.1	c.3204C>G	p.Asp1068Glu	missense_variant	Exon 54 of 88	ENST00000295246.7	NP_001380911.1
ANKRD36C	NM_001310154.3	c.3279C>G	p.Asp1093Glu	missense_variant	Exon 55 of 89		NP_001297083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD36C	ENST00000295246.7	c.3204C>G	p.Asp1068Glu	missense_variant	Exon 54 of 88	5	NM_001393982.1	ENSP00000295246.7
ANKRD36C	ENST00000456556.5	c.2654-3611C>G		intron_variant	Intron 42 of 66	5		ENSP00000403302.1
ANKRD36C	ENST00000531153.5	n.985C>G		non_coding_transcript_exon_variant	Exon 7 of 31	5
ANKRD36C	ENST00000534304.5	n.*982-3611C>G		intron_variant	Intron 24 of 42	5		ENSP00000433685.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000139 AC: 2 AN: 1437730 Hom.: 0 Cov.: 32 AF XY: 0.00000140 AC XY: 1 AN XY: 714198

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000237

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.074
DANN	Benign	0.33
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-96568695;