rs270487

Positions:

• chr1-70276380-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030816.5(ANKRD13C):​c.1295+385C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,866 control chromosomes in the GnomAD database, including 15,719 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (15719 hom., cov: 31)
• Consequence: ANKRD13C NM_030816.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

Genes affected

ANKRD13C (HGNC:25374): (ankyrin repeat domain 13C) Enables signaling receptor binding activity. Involved in protein retention in ER lumen; regulation of anoikis; and regulation of signaling receptor activity. Located in perinuclear region of cytoplasm. Colocalizes with endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD13C	NM_030816.5	c.1295+385C>G		intron_variant		ENST00000370944.9	NP_110443.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD13C	ENST00000370944.9	c.1295+385C>G		intron_variant		1	NM_030816.5	ENSP00000359982	P1
ANKRD13C	ENST00000262346.6	c.1190+385C>G		intron_variant		1		ENSP00000262346
ANKRD13C	ENST00000464236.1	n.79+385C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68242 AN: 151748 Hom.: 15687 Cov.: 31

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.423

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.450 AC: 68321 AN: 151866 Hom.: 15719 Cov.: 31 AF XY: 0.453 AC XY: 33597 AN XY: 74226

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.427

Alfa AF: 0.432 Hom.: 1796

Bravo AF: 0.449

Asia WGS AF: 0.559 AC: 1942 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.51

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: rs270487; hg19: chr1-70742063; COSMIC: COSV52029991;