rs6702883

Variant names:

• chr1-104700458-A-G
• rs6702883

Your query was ambiguous. Multiple possible variants found:

• chr1-104700458-A-G
• chr1-104700458-A-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 0.403 in 151,688 control chromosomes in the GnomAD database, including 14,253 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 0.40 (14253 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 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: 0.404 AC: 61190 AN: 151570 Hom.: 14264 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.403 AC: 61179 AN: 151688 Hom.: 14253 Cov.: 31 AF XY: 0.403 AC XY: 29889 AN XY: 74134

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.378

Alfa AF: 0.463 Hom.: 6913

Bravo AF: 0.371

Asia WGS AF: 0.267 AC: 921 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6702883; hg19: chr1-105243080;