4-74090655-A-T

Variant names:

• chr4-74090655-A-T
• rs546829

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 0.626 in 151,942 control chromosomes in the GnomAD database, including 29,901 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 0.63 (29901 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.691 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: 0.626 AC: 95075 AN: 151824 Hom.: 29874 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.626 AC: 95153 AN: 151942 Hom.: 29901 Cov.: 31 AF XY: 0.631 AC XY: 46835 AN XY: 74252

African (AFR) AF: 0.604 AC: 25021 AN: 41414

American (AMR) AF: 0.703 AC: 10732 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2159 AN: 3466

East Asian (EAS) AF: 0.490 AC: 2522 AN: 5142

South Asian (SAS) AF: 0.669 AC: 3220 AN: 4810

European-Finnish (FIN) AF: 0.685 AC: 7236 AN: 10564

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42153 AN: 67948

Other (OTH) AF: 0.625 AC: 1323 AN: 2116

Alfa AF: 0.617 Hom.: 16074

Bravo AF: 0.626

Asia WGS AF: 0.586 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.87
DANN	Benign	0.56
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs546829; hg19: chr4-74956372;