4-174541479-C-A

Variant names:

• chr4-174541479-C-A
• rs9990951

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 0.297 in 151,972 control chromosomes in the GnomAD database, including 7,042 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 0.30 (7042 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.297 AC: 45046 AN: 151852 Hom.: 7025 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.297 AC: 45112 AN: 151972 Hom.: 7042 Cov.: 33 AF XY: 0.297 AC XY: 22084 AN XY: 74286

African (AFR) AF: 0.392 AC: 16249 AN: 41436

American (AMR) AF: 0.252 AC: 3852 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 748 AN: 3472

East Asian (EAS) AF: 0.264 AC: 1362 AN: 5168

South Asian (SAS) AF: 0.230 AC: 1111 AN: 4826

European-Finnish (FIN) AF: 0.326 AC: 3433 AN: 10528

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17491 AN: 67932

Other (OTH) AF: 0.285 AC: 602 AN: 2112

Alfa AF: 0.259 Hom.: 6479

Bravo AF: 0.295

Asia WGS AF: 0.272 AC: 943 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.30
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs9990951; hg19: chr4-175462630;