rs1561164

Variant names:

• chr3-87076876-G-A
• rs1561164

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 0.0442 in 151,968 control chromosomes in the GnomAD database, including 193 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 0.044 (193 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0844 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: 0.0441 AC: 6692 AN: 151850 Hom.: 191 Cov.: 32

Gnomad AFR AF: 0.0865

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0305

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0340

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0304

Gnomad OTH AF: 0.0436

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

GnomAD4 genome AF: 0.0442 AC: 6713 AN: 151968 Hom.: 193 Cov.: 32 AF XY: 0.0434 AC XY: 3224 AN XY: 74276

Gnomad4 AFR AF: 0.0867

Gnomad4 AMR AF: 0.0306

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.0340

Gnomad4 NFE AF: 0.0304

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0326 Hom.: 27

Bravo AF: 0.0463

Asia WGS AF: 0.0230 AC: 79 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1561164; hg19: chr3-87126026;