chr1-8313148-A-G

Variant names:

• chr1-8313148-A-G
• rs966134

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 0.554 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
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.317 AC: 13171 AN: 41490

American (AMR) AF: 0.644 AC: 9846 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1895 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3927 AN: 5176

South Asian (SAS) AF: 0.491 AC: 2370 AN: 4828

European-Finnish (FIN) AF: 0.731 AC: 7738 AN: 10588

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43437 AN: 67986

Other (OTH) AF: 0.546 AC: 1152 AN: 2110

Alfa AF: 0.607 Hom.: 120615

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs966134; hg19: chr1-8373208;