rs660895

Positions:

• chr6-32609603-A-G

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 0.195 in 152,160 control chromosomes in the GnomAD database, including 3,142 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 0.20 (3142 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29656 AN: 152042 Hom.: 3133 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.195 AC: 29694 AN: 152160 Hom.: 3142 Cov.: 31 AF XY: 0.199 AC XY: 14798 AN XY: 74396

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.171

Alfa AF: 0.194 Hom.: 4728

Bravo AF: 0.202

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs660895; hg19: chr6-32577380;