chr2-95855406-C-T

Variant names:

• chr2-95855406-C-T
• NM_001393982.1:c.5878G>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001393982.1(ANKRD36C):​c.5878G>A​(p.Asp1960Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1960H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: ANKRD36C NM_001393982.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

Genes affected

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

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08229798).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36C	NM_001393982.1	c.5878G>A	p.Asp1960Asn	missense_variant	Exon 83 of 88	ENST00000295246.7	NP_001380911.1
ANKRD36C	NM_001310154.3	c.5953G>A	p.Asp1985Asn	missense_variant	Exon 84 of 89		NP_001297083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD36C	ENST00000295246.7	c.5878G>A	p.Asp1960Asn	missense_variant	Exon 83 of 88	5	NM_001393982.1	ENSP00000295246.7
ANKRD36C	ENST00000488721.5	n.1028G>A		non_coding_transcript_exon_variant	Exon 3 of 4	1
ANKRD36C	ENST00000456556.5	c.4855G>A	p.Asp1619Asn	missense_variant	Exon 63 of 67	5		ENSP00000403302.1
ANKRD36C	ENST00000612359.4	c.-69G>A		upstream_gene_variant		1		ENSP00000485004.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1461186 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 726874

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000270

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.39	T
BayesDel_noAF	Benign	-0.80
CADD	Benign	17
DANN	Uncertain	0.99
DEOGEN2	Benign	0.00071	T
Eigen	Benign	-0.63
Eigen_PC	Benign	-0.74
FATHMM_MKL	Benign	0.11	N
LIST_S2	Benign	0.40	T
M_CAP	Benign	0.0012	T
MetaRNN	Benign	0.082	T
MetaSVM	Benign	-0.94	T
PROVEAN	Benign	-0.070	N
REVEL	Benign	0.059
Sift	Benign	0.15	T
Sift4G	Benign	0.11	T
Vest4		0.063
MutPred		0.17		Gain of MoRF binding (P = 0.0301);
MVP		0.076
ClinPred		0.17	T
GERP RS		-0.83
Varity_R		0.040
gMVP		0.0094

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: chr2-96521154;