1-153647610-A-G

Variant names:

• chr1-153647610-A-G
• rs913859

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 0.918 in 152,220 control chromosomes in the GnomAD database, including 64,405 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 0.92 (64405 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.918 AC: 139676 AN: 152102 Hom.: 64344 Cov.: 32

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.918 AC: 139797 AN: 152220 Hom.: 64405 Cov.: 32 AF XY: 0.921 AC XY: 68567 AN XY: 74420

African (AFR) AF: 0.979 AC: 40652 AN: 41544

American (AMR) AF: 0.940 AC: 14379 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2961 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5162 AN: 5166

South Asian (SAS) AF: 0.971 AC: 4688 AN: 4830

European-Finnish (FIN) AF: 0.880 AC: 9320 AN: 10586

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59615 AN: 68010

Other (OTH) AF: 0.915 AC: 1931 AN: 2110

Alfa AF: 0.891 Hom.: 111756

Bravo AF: 0.924

Asia WGS AF: 0.983 AC: 3418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs913859; hg19: chr1-153620086;