chr1-104700458-A-G

Variant names:

• chr1-104700458-A-G
• rs6702883

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 0.403 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.194 AC: 8018 AN: 41430

American (AMR) AF: 0.344 AC: 5234 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1858 AN: 3466

East Asian (EAS) AF: 0.163 AC: 842 AN: 5174

South Asian (SAS) AF: 0.357 AC: 1723 AN: 4820

European-Finnish (FIN) AF: 0.617 AC: 6439 AN: 10428

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35749 AN: 67844

Other (OTH) AF: 0.378 AC: 795 AN: 2102

Alfa AF: 0.468 Hom.: 7917

Bravo AF: 0.371

Asia WGS AF: 0.267 AC: 921 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.76
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs6702883; hg19: chr1-105243080;