rs629566

Variant names:

• chr9-32573604-T-C
• rs629566

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 0.233 in 152,132 control chromosomes in the GnomAD database, including 4,368 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 0.23 (4368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.233 AC: 35412 AN: 152014 Hom.: 4363 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.0972

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.233 AC: 35419 AN: 152132 Hom.: 4368 Cov.: 32 AF XY: 0.228 AC XY: 16935 AN XY: 74370

African (AFR) AF: 0.265 AC: 11000 AN: 41492

American (AMR) AF: 0.198 AC: 3020 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3468

East Asian (EAS) AF: 0.00444 AC: 23 AN: 5180

South Asian (SAS) AF: 0.0975 AC: 470 AN: 4822

European-Finnish (FIN) AF: 0.217 AC: 2291 AN: 10578

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17274 AN: 67992

Other (OTH) AF: 0.225 AC: 475 AN: 2110

Alfa AF: 0.243 Hom.: 2772

Bravo AF: 0.231

Asia WGS AF: 0.0570 AC: 198 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	4.6
DANN	Benign	0.80
PhyloP100		-0.14
PromoterAI		0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs629566; hg19: chr9-32573602; COSMIC: COSV63083207;