rs4610776

chr8-7057155-A-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 0.261 in 152,056 control chromosomes in the GnomAD database, including 5,339 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 0.26 (5339 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39600 AN: 151940 Hom.: 5330 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.261 AC: 39641 AN: 152056 Hom.: 5339 Cov.: 31 AF XY: 0.256 AC XY: 19022 AN XY: 74354

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0741

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.249

Alfa AF: 0.264 Hom.: 711

Bravo AF: 0.259

Asia WGS AF: 0.138 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.5
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4610776; hg19: chr8-6914677;