rs1425609

Variant names:

• chr3-162964207-G-A
• rs1425609

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.369 in 151,958 control chromosomes in the GnomAD database, including 10,498 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 0.37 (10498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 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: 0.369 AC: 55989 AN: 151840 Hom.: 10486 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.369 AC: 56032 AN: 151958 Hom.: 10498 Cov.: 32 AF XY: 0.376 AC XY: 27943 AN XY: 74242

African (AFR) AF: 0.355 AC: 14710 AN: 41402

American (AMR) AF: 0.339 AC: 5181 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1121 AN: 3460

East Asian (EAS) AF: 0.172 AC: 888 AN: 5172

South Asian (SAS) AF: 0.478 AC: 2303 AN: 4822

European-Finnish (FIN) AF: 0.497 AC: 5240 AN: 10544

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25382 AN: 67970

Other (OTH) AF: 0.321 AC: 678 AN: 2112

Alfa AF: 0.370 Hom.: 14195

Bravo AF: 0.355

Asia WGS AF: 0.306 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.8
DANN	Benign	0.44
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1425609; hg19: chr3-162681995;