rs4958849

Variant names:

• chr5-150294411-G-A
• rs4958849

Your query was ambiguous. Multiple possible variants found:

• chr5-150294411-G-A
• chr5-150294411-G-C
• chr5-150294411-G-T

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 0.74 in 152,002 control chromosomes in the GnomAD database, including 43,611 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 0.74 (43611 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.867 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: 0.740 AC: 112407 AN: 151884 Hom.: 43616 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.740 AC: 112436 AN: 152002 Hom.: 43611 Cov.: 31 AF XY: 0.738 AC XY: 54830 AN XY: 74270

African (AFR) AF: 0.490 AC: 20305 AN: 41426

American (AMR) AF: 0.708 AC: 10831 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2824 AN: 3468

East Asian (EAS) AF: 0.724 AC: 3729 AN: 5154

South Asian (SAS) AF: 0.791 AC: 3807 AN: 4810

European-Finnish (FIN) AF: 0.850 AC: 8987 AN: 10576

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59346 AN: 67962

Other (OTH) AF: 0.751 AC: 1584 AN: 2110

Alfa AF: 0.801 Hom.: 12561

Bravo AF: 0.716

Asia WGS AF: 0.735 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.79
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs4958849; hg19: chr5-149673974;