rs6695567

Variant names:

• chr1-53163913-G-A
• rs6695567

Your query was ambiguous. Multiple possible variants found:

• chr1-53163913-G-A
• chr1-53163913-G-C
• chr1-53163913-G-T

Variant summary

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

The variant allele was found at a frequency of 0.52 in 151,864 control chromosomes in the GnomAD database, including 21,854 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 0.52 (21854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

ACMG classification

Verdict is Benign. Variant got -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 = 0.708 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: 0.520 AC: 78848 AN: 151748 Hom.: 21824 Cov.: 32

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.520 AC: 78918 AN: 151864 Hom.: 21854 Cov.: 32 AF XY: 0.517 AC XY: 38364 AN XY: 74194

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.522

Alfa AF: 0.433 Hom.: 32646

Bravo AF: 0.552

Asia WGS AF: 0.439 AC: 1528 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	1.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6695567; hg19: chr1-53629585;