rs667660

Variant names:

• chr7-99821603-T-G
• rs667660

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 0.243 in 152,160 control chromosomes in the GnomAD database, including 10,102 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 0.24 (10102 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 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: 0.243 AC: 36905 AN: 152040 Hom.: 10064 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0766

Gnomad FIN AF: 0.0583

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.243 AC: 37002 AN: 152160 Hom.: 10102 Cov.: 32 AF XY: 0.236 AC XY: 17579 AN XY: 74400

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.0879

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0768

Gnomad4 FIN AF: 0.0583

Gnomad4 NFE AF: 0.0705

Gnomad4 OTH AF: 0.206

Alfa AF: 0.0919 Hom.: 2709

Bravo AF: 0.269

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs667660; hg19: chr7-99419226;