chr4-13241173-G-A

Variant names:

• chr4-13241173-G-A
• rs733048

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 0.212 in 152,006 control chromosomes in the GnomAD database, including 3,674 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 0.21 (3674 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32203 AN: 151890 Hom.: 3669 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.212 AC: 32223 AN: 152006 Hom.: 3674 Cov.: 32 AF XY: 0.214 AC XY: 15863 AN XY: 74256

African (AFR) AF: 0.133 AC: 5533 AN: 41458

American (AMR) AF: 0.244 AC: 3730 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1088 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1815 AN: 5138

South Asian (SAS) AF: 0.194 AC: 933 AN: 4810

European-Finnish (FIN) AF: 0.253 AC: 2673 AN: 10560

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15669 AN: 67972

Other (OTH) AF: 0.243 AC: 512 AN: 2106

Alfa AF: 0.225 Hom.: 7609

Bravo AF: 0.209

Asia WGS AF: 0.280 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.34
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs733048; hg19: chr4-13242797;