4-46031408-G-T

Variant names:

• chr4-46031408-G-T
• rs954039

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 0.0592 in 151,964 control chromosomes in the GnomAD database, including 464 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 0.059 (464 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 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: 0.0590 AC: 8957 AN: 151852 Hom.: 458 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.0729

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0201

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0592 AC: 8990 AN: 151964 Hom.: 464 Cov.: 32 AF XY: 0.0617 AC XY: 4584 AN XY: 74292

African (AFR) AF: 0.130 AC: 5377 AN: 41330

American (AMR) AF: 0.0830 AC: 1267 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3464

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0114 AC: 55 AN: 4816

European-Finnish (FIN) AF: 0.0729 AC: 772 AN: 10594

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0201 AC: 1367 AN: 68010

Other (OTH) AF: 0.0436 AC: 92 AN: 2112

Alfa AF: 0.0347 Hom.: 85

Bravo AF: 0.0621

Asia WGS AF: 0.0230 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.24
DANN	Benign	0.37
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs954039; hg19: chr4-46033425;