rs7755766

Variant names:

• chr6-15675410-T-C
• rs7755766

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 0.133 in 152,152 control chromosomes in the GnomAD database, including 1,429 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 0.13 (1429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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: 0.133 AC: 20183 AN: 152034 Hom.: 1426 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0925

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.133 AC: 20207 AN: 152152 Hom.: 1429 Cov.: 32 AF XY: 0.131 AC XY: 9738 AN XY: 74398

African (AFR) AF: 0.139 AC: 5755 AN: 41484

American (AMR) AF: 0.106 AC: 1619 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0925 AC: 321 AN: 3472

East Asian (EAS) AF: 0.0217 AC: 112 AN: 5168

South Asian (SAS) AF: 0.142 AC: 686 AN: 4830

European-Finnish (FIN) AF: 0.114 AC: 1205 AN: 10594

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10099 AN: 68000

Other (OTH) AF: 0.135 AC: 284 AN: 2110

Alfa AF: 0.139 Hom.: 1995

Bravo AF: 0.132

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.59
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs7755766; hg19: chr6-15675641;