rs248158

Variant names:

• chr5-135958381-C-T
• rs248158

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.618 in 152,066 control chromosomes in the GnomAD database, including 29,218 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 0.62 (29218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.668 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: 0.618 AC: 93902 AN: 151948 Hom.: 29195 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.618 AC: 93960 AN: 152066 Hom.: 29218 Cov.: 32 AF XY: 0.619 AC XY: 46040 AN XY: 74342

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.609

Alfa AF: 0.614 Hom.: 3563

Bravo AF: 0.616

Asia WGS AF: 0.666 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs248158; hg19: chr5-135294070; COSMIC: COSV50846898;