rs660895

Variant names:

• chr6-32609603-A-G
• rs660895

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 0.195 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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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 AC: 0.145723 AN: 0.145723

Gnomad4 AMR AF: 0.291 AC: 0.29128 AN: 0.29128

Gnomad4 ASJ AF: 0.211 AC: 0.211361 AN: 0.211361

Gnomad4 EAS AF: 0.268 AC: 0.267505 AN: 0.267505

Gnomad4 SAS AF: 0.128 AC: 0.127849 AN: 0.127849

Gnomad4 FIN AF: 0.254 AC: 0.254208 AN: 0.254208

Gnomad4 NFE AF: 0.194 AC: 0.193731 AN: 0.193731

Gnomad4 OTH AF: 0.171 AC: 0.170778 AN: 0.170778

Alfa AF: 0.203 Hom.: 14472

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;