rs501871

Variant names:

• chr6-24000499-A-G
• rs501871

Your query was ambiguous. Multiple possible variants found:

• chr6-24000499-A-G
• chr6-24000499-A-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 0.388 in 151,882 control chromosomes in the GnomAD database, including 11,698 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 0.39 (11698 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58948 AN: 151762 Hom.: 11686 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.388 AC: 58992 AN: 151882 Hom.: 11698 Cov.: 32 AF XY: 0.388 AC XY: 28811 AN XY: 74212

African (AFR) AF: 0.434 AC: 17983 AN: 41458

American (AMR) AF: 0.278 AC: 4243 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1065 AN: 5150

South Asian (SAS) AF: 0.465 AC: 2239 AN: 4814

European-Finnish (FIN) AF: 0.376 AC: 3953 AN: 10514

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26800 AN: 67910

Other (OTH) AF: 0.395 AC: 832 AN: 2104

Alfa AF: 0.390 Hom.: 5022

Bravo AF: 0.378

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.1
DANN	Benign	0.83
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs501871; hg19: chr6-24000727;