chr1-153647610-A-G

Variant names:

• chr1-153647610-A-G
• rs913859

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 0.918 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.979

Gnomad4 AMR AF: 0.940

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.971

Gnomad4 FIN AF: 0.880

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.915

Alfa AF: 0.886 Hom.: 79468

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs913859; hg19: chr1-153620086;