5-135957562-T-C

Variant names:

• chr5-135957562-T-C
• rs248163

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 0.792 in 151,658 control chromosomes in the GnomAD database, including 48,256 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 0.79 (48256 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.791 AC: 119917 AN: 151540 Hom.: 48189 Cov.: 29

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.792 AC: 120039 AN: 151658 Hom.: 48256 Cov.: 29 AF XY: 0.793 AC XY: 58737 AN XY: 74094

African (AFR) AF: 0.943 AC: 39017 AN: 41396

American (AMR) AF: 0.767 AC: 11674 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2591 AN: 3470

East Asian (EAS) AF: 0.786 AC: 4051 AN: 5152

South Asian (SAS) AF: 0.812 AC: 3903 AN: 4806

European-Finnish (FIN) AF: 0.752 AC: 7847 AN: 10432

Middle Eastern (MID) AF: 0.760 AC: 222 AN: 292

European-Non Finnish (NFE) AF: 0.714 AC: 48436 AN: 67880

Other (OTH) AF: 0.763 AC: 1601 AN: 2098

Alfa AF: 0.758 Hom.: 12707

Bravo AF: 0.799

Asia WGS AF: 0.803 AC: 2788 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.61
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs248163; hg19: chr5-135293251;