rs1014604

Variant names:

• chr21-16968742-G-A
• rs1014604

Your query was ambiguous. Multiple possible variants found:

• chr21-16968742-G-A
• chr21-16968742-G-C
• chr21-16968742-G-T

Variant summary

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

The variant allele was found at a frequency of 0.611 in 152,002 control chromosomes in the GnomAD database, including 30,034 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 0.61 (30034 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92795 AN: 151884 Hom.: 29997 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.611 AC: 92882 AN: 152002 Hom.: 30034 Cov.: 32 AF XY: 0.611 AC XY: 45355 AN XY: 74274

African (AFR) AF: 0.848 AC: 35212 AN: 41504

American (AMR) AF: 0.573 AC: 8740 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1748 AN: 3468

East Asian (EAS) AF: 0.506 AC: 2609 AN: 5156

South Asian (SAS) AF: 0.448 AC: 2159 AN: 4824

European-Finnish (FIN) AF: 0.545 AC: 5746 AN: 10548

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34855 AN: 67936

Other (OTH) AF: 0.571 AC: 1207 AN: 2112

Alfa AF: 0.536 Hom.: 95971

Bravo AF: 0.620

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.7
DANN	Benign	0.21
PhyloP100		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1014604; hg19: chr21-18341062;