rs182623

Variant names:

• chr6-52997060-A-T
• rs182623

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 0.315 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.463 AC: 18832 AN: 40660

American (AMR) AF: 0.256 AC: 3855 AN: 15064

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1122 AN: 3464

East Asian (EAS) AF: 0.130 AC: 662 AN: 5080

South Asian (SAS) AF: 0.167 AC: 792 AN: 4754

European-Finnish (FIN) AF: 0.271 AC: 2784 AN: 10260

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18410 AN: 67704

Other (OTH) AF: 0.308 AC: 642 AN: 2084

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs182623; hg19: chr6-52861858;