rs1538972

chr1-161706767-G-Achr1-161706767-G-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 0.836 in 152,178 control chromosomes in the GnomAD database, including 53,451 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 0.84 (53451 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

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 = 0.947 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: 0.836 AC: 127190 AN: 152060 Hom.: 53417 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.836 AC: 127275 AN: 152178 Hom.: 53451 Cov.: 31 AF XY: 0.840 AC XY: 62487 AN XY: 74396

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.868

Alfa AF: 0.843 Hom.: 73545

Bravo AF: 0.834

Asia WGS AF: 0.907 AC: 3155 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	2.2
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1538972; hg19: chr1-161676557;