rs1425967

Positions:

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

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 0.522 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.483

Alfa AF: 0.501 Hom.: 4565

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1425967; hg19: chr4-138288890;