rs2050632

Variant names:

• chr1-244996265-C-T
• rs2050632
• NM_032328.4:c.26-20977C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032328.4(DRC8):​c.26-20977C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,316 control chromosomes in the GnomAD database, including 26,507 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 0.59 (26507 hom., cov: 29)
• Consequence: DRC8 NM_032328.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 14 publications found

Genes affected

DRC8 (HGNC:28166): (EF-hand calcium binding domain 2) The gene encodes a protein that contains two EF-hand calcium-binding domains although its function has yet to be determined. Alternatively spliced transcripts have been observed. [provided by RefSeq, Mar 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRC8	NM_032328.4	c.26-20977C>T		intron_variant	Intron 2 of 7	ENST00000366523.6	NP_115704.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB2	ENST00000366523.6	c.26-20977C>T		intron_variant	Intron 2 of 7	3	NM_032328.4	ENSP00000355480.1

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88536 AN: 151198 Hom.: 26480 Cov.: 29

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.586 AC: 88607 AN: 151316 Hom.: 26507 Cov.: 29 AF XY: 0.592 AC XY: 43748 AN XY: 73874

African (AFR) AF: 0.457 AC: 18842 AN: 41200

American (AMR) AF: 0.635 AC: 9600 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2218 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3838 AN: 5150

South Asian (SAS) AF: 0.693 AC: 3311 AN: 4780

European-Finnish (FIN) AF: 0.682 AC: 7125 AN: 10444

Middle Eastern (MID) AF: 0.576 AC: 167 AN: 290

European-Non Finnish (NFE) AF: 0.615 AC: 41708 AN: 67870

Other (OTH) AF: 0.595 AC: 1243 AN: 2090

Alfa AF: 0.617 Hom.: 15352

Bravo AF: 0.574

Asia WGS AF: 0.717 AC: 2492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.92
DANN	Benign	0.37
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2050632; hg19: chr1-245159567;