rs6765660

Variant names:

• chr3-154559627-T-G
• rs6765660

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 0.23 in 152,042 control chromosomes in the GnomAD database, including 6,380 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 (6380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 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: 0.230 AC: 34891 AN: 151924 Hom.: 6342 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.230 AC: 34989 AN: 152042 Hom.: 6380 Cov.: 32 AF XY: 0.225 AC XY: 16753 AN XY: 74322

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0790

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.215

Alfa AF: 0.186 Hom.: 516

Bravo AF: 0.248

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6765660; hg19: chr3-154277416;