rs182623

Variant names:

• chr6-52997060-A-T
• rs182623

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 0.315 in 150,268 control chromosomes in the GnomAD database, including 8,284 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 0.31 (8284 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 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: 0.315 AC: 47227 AN: 150148 Hom.: 8240 Cov.: 27

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.340

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.315 AC: 47306 AN: 150268 Hom.: 8284 Cov.: 27 AF XY: 0.309 AC XY: 22627 AN XY: 73258

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.308

Alfa AF: 0.310 Hom.: 977

Bravo AF: 0.323

Asia WGS AF: 0.158 AC: 548 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs182623; hg19: chr6-52861858;