rs966134

chr1-8313148-A-Gchr1-8313148-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 0.554 in 152,132 control chromosomes in the GnomAD database, including 25,234 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 0.55 (25234 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.554 AC: 84268 AN: 152014 Hom.: 25231 Cov.: 33

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.554 AC: 84295 AN: 152132 Hom.: 25234 Cov.: 33 AF XY: 0.560 AC XY: 41645 AN XY: 74376

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.546

Alfa AF: 0.616 Hom.: 58756

Bravo AF: 0.542

Asia WGS AF: 0.559 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.1
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs966134; hg19: chr1-8373208;