rs1572970

Variant names:

• chr1-159703795-G-A
• rs1572970

Your query was ambiguous. Multiple possible variants found:

• chr1-159703795-G-A
• chr1-159703795-G-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 0.612 in 151,974 control chromosomes in the GnomAD database, including 30,582 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 0.61 (30582 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.824

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.726 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: 0.612 AC: 92991 AN: 151856 Hom.: 30568 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.612 AC: 93033 AN: 151974 Hom.: 30582 Cov.: 31 AF XY: 0.616 AC XY: 45777 AN XY: 74308

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.638

Alfa AF: 0.695 Hom.: 48896

Bravo AF: 0.602

Asia WGS AF: 0.618 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1572970; hg19: chr1-159673585;