chr1-8257898-A-C

Position:

• chr1-8257898-A-C

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 0.774 in 151,400 control chromosomes in the GnomAD database, including 45,615 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 0.77 (45615 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 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: 0.774 AC: 117061 AN: 151282 Hom.: 45596 Cov.: 27

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.774 AC: 117139 AN: 151400 Hom.: 45615 Cov.: 27 AF XY: 0.769 AC XY: 56832 AN XY: 73920

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.755

Alfa AF: 0.783 Hom.: 7899

Bravo AF: 0.768

Asia WGS AF: 0.637 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7520292; hg19: chr1-8317958;