rs1426409

Positions:

• chr4-37172322-G-A
• chr4-37172322-G-C

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 0.76 in 152,038 control chromosomes in the GnomAD database, including 44,263 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 0.76 (44263 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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 = 0.969 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: 0.760 AC: 115447 AN: 151920 Hom.: 44210 Cov.: 31

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.760 AC: 115566 AN: 152038 Hom.: 44263 Cov.: 31 AF XY: 0.760 AC XY: 56485 AN XY: 74320

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.737

Alfa AF: 0.692 Hom.: 3639

Bravo AF: 0.777

Asia WGS AF: 0.869 AC: 3022 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	1.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1426409; hg19: chr4-37173944;