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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.388 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

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.395

Alfa AF: 0.390 Hom.: 2690

Bravo AF: 0.378

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs501871; hg19: chr6-24000727;