rs1425967

Variant names:

• chr4-137367736-A-G
• rs1425967

Your query was ambiguous. Multiple possible variants found:

• chr4-137367736-A-G
• chr4-137367736-A-T

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 0.522 in 152,136 control chromosomes in the GnomAD database, including 21,547 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 0.52 (21547 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 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: 0.522 AC: 79347 AN: 152018 Hom.: 21530 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.522 AC: 79409 AN: 152136 Hom.: 21547 Cov.: 33 AF XY: 0.521 AC XY: 38732 AN XY: 74382

African (AFR) AF: 0.679 AC: 28167 AN: 41504

American (AMR) AF: 0.557 AC: 8507 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3472

East Asian (EAS) AF: 0.533 AC: 2758 AN: 5178

South Asian (SAS) AF: 0.322 AC: 1553 AN: 4824

European-Finnish (FIN) AF: 0.506 AC: 5361 AN: 10588

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30137 AN: 67972

Other (OTH) AF: 0.483 AC: 1021 AN: 2112

Alfa AF: 0.498 Hom.: 7806

Bravo AF: 0.536

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs1425967; hg19: chr4-138288890;