rs760607

Variant names:

• chr1-23536161-A-G
• rs760607

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 0.452 in 152,080 control chromosomes in the GnomAD database, including 16,355 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 0.45 (16355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 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: 0.452 AC: 68703 AN: 151962 Hom.: 16350 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.452 AC: 68742 AN: 152080 Hom.: 16355 Cov.: 32 AF XY: 0.460 AC XY: 34164 AN XY: 74336

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.452

Alfa AF: 0.417 Hom.: 4580

Bravo AF: 0.455

Asia WGS AF: 0.684 AC: 2376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs760607; hg19: chr1-23862653;