rs6702463

Variant names:

• chr1-152626235-T-A
• rs6702463

Your query was ambiguous. Multiple possible variants found:

• chr1-152626235-T-A
• chr1-152626235-T-G

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 0.667 in 152,194 control chromosomes in the GnomAD database, including 33,945 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 0.67 (33945 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 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: 0.667 AC: 101443 AN: 152076 Hom.: 33907 Cov.: 34

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.667 AC: 101531 AN: 152194 Hom.: 33945 Cov.: 34 AF XY: 0.669 AC XY: 49740 AN XY: 74398

African (AFR) AF: 0.726 AC: 30157 AN: 41530

American (AMR) AF: 0.653 AC: 9990 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2161 AN: 3472

East Asian (EAS) AF: 0.613 AC: 3176 AN: 5178

South Asian (SAS) AF: 0.632 AC: 3053 AN: 4830

European-Finnish (FIN) AF: 0.662 AC: 7004 AN: 10576

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43948 AN: 68004

Other (OTH) AF: 0.633 AC: 1336 AN: 2110

Alfa AF: 0.658 Hom.: 4101

Bravo AF: 0.665

Asia WGS AF: 0.602 AC: 2094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs6702463; hg19: chr1-152598711;