chr1-70319252-T-C

Variant names:

• chr1-70319252-T-C
• rs12737233
• NM_030816.5:c.578-3686A>G

Variant summary

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

The NM_030816.5(ANKRD13C):​c.578-3686A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,192 control chromosomes in the GnomAD database, including 1,054 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 0.11 (1054 hom., cov: 31)
• Consequence: ANKRD13C NM_030816.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD13C	NM_030816.5	c.578-3686A>G		intron_variant	Intron 3 of 12	ENST00000370944.9	NP_110443.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD13C	ENST00000370944.9	c.578-3686A>G		intron_variant	Intron 3 of 12	1	NM_030816.5	ENSP00000359982.4
ANKRD13C	ENST00000262346.6	c.473-3686A>G		intron_variant	Intron 2 of 11	1		ENSP00000262346.6
ANKRD13C	ENST00000498735.1	n.106-3686A>G		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16036 AN: 152074 Hom.: 1052 Cov.: 31

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.0746

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.105 AC: 16038 AN: 152192 Hom.: 1054 Cov.: 31 AF XY: 0.104 AC XY: 7704 AN XY: 74412

Gnomad4 AFR AF: 0.0281

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0854

Gnomad4 SAS AF: 0.0753

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.119

Alfa AF: 0.127 Hom.: 661

Bravo AF: 0.100

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.72

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: rs12737233; hg19: chr1-70784935;