rs2766554

Positions:

• chr6-35751550-C-T

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 0.569 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.549

Alfa AF: 0.555 Hom.: 4640

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2766554; hg19: chr6-35719327;