rs6902723

chr6-32764183-G-Achr6-32764183-G-Cchr6-32764183-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 0.551 in 151,942 control chromosomes in the GnomAD database, including 23,483 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 0.55 (23483 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83718 AN: 151822 Hom.: 23463 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.551 AC: 83793 AN: 151942 Hom.: 23483 Cov.: 32 AF XY: 0.556 AC XY: 41268 AN XY: 74254

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.601

Alfa AF: 0.509 Hom.: 17439

Bravo AF: 0.564

Asia WGS AF: 0.620 AC: 2152 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.0
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6902723; hg19: chr6-32731960;