4-37172322-G-A

Variant names:

• chr4-37172322-G-A
• rs1426409
• ENST00000719984.1:n.167-18234C>T

Variant summary

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

The ENST00000719984.1(ENSG00000293926):​n.167-18234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000293926 ENST00000719984.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 7 publications found

Genes affected

ENSG00000293926 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293926	ENST00000719984.1	n.167-18234C>T		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.803 AC: 33316 AN: 41494

American (AMR) AF: 0.813 AC: 12402 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2351 AN: 3454

East Asian (EAS) AF: 0.991 AC: 5137 AN: 5182

South Asian (SAS) AF: 0.780 AC: 3769 AN: 4830

European-Finnish (FIN) AF: 0.673 AC: 7098 AN: 10540

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49148 AN: 67964

Other (OTH) AF: 0.737 AC: 1558 AN: 2114

Alfa AF: 0.712 Hom.: 9210

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1426409; hg19: chr4-37173944;