rs602875

Variant names:

• chr6-32605852-A-G
• rs602875

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 0.269 in 151,808 control chromosomes in the GnomAD database, including 5,832 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 0.27 (5832 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 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: 0.269 AC: 40771 AN: 151690 Hom.: 5828 Cov.: 29

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.269 AC: 40801 AN: 151808 Hom.: 5832 Cov.: 29 AF XY: 0.267 AC XY: 19784 AN XY: 74170

African (AFR) AF: 0.310 AC: 12800 AN: 41350

American (AMR) AF: 0.255 AC: 3892 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3468

East Asian (EAS) AF: 0.381 AC: 1966 AN: 5154

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4800

European-Finnish (FIN) AF: 0.208 AC: 2194 AN: 10526

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17053 AN: 67934

Other (OTH) AF: 0.279 AC: 589 AN: 2110

Alfa AF: 0.255 Hom.: 7729

Bravo AF: 0.273

Asia WGS AF: 0.266 AC: 926 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.84
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs602875; hg19: chr6-32573629;