rs2766554

Variant names:

• chr6-35751550-C-T
• rs2766554

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 0.569 in 152,062 control chromosomes in the GnomAD database, including 25,981 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 0.57 (25981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 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: 0.569 AC: 86442 AN: 151944 Hom.: 25923 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.569 AC: 86560 AN: 152062 Hom.: 25981 Cov.: 32 AF XY: 0.569 AC XY: 42272 AN XY: 74302

African (AFR) AF: 0.776 AC: 32224 AN: 41510

American (AMR) AF: 0.483 AC: 7374 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1877 AN: 3466

East Asian (EAS) AF: 0.384 AC: 1982 AN: 5166

South Asian (SAS) AF: 0.542 AC: 2608 AN: 4814

European-Finnish (FIN) AF: 0.534 AC: 5639 AN: 10558

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33123 AN: 67964

Other (OTH) AF: 0.549 AC: 1157 AN: 2108

Alfa AF: 0.538 Hom.: 8225

Bravo AF: 0.570

Asia WGS AF: 0.525 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.36
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs2766554; hg19: chr6-35719327;