rs248166

Variant names:

• chr5-135957019-G-A
• rs248166

Your query was ambiguous. Multiple possible variants found:

• chr5-135957019-G-A
• chr5-135957019-G-C

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 0.792 in 152,180 control chromosomes in the GnomAD database, including 48,431 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 (48431 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 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: 0.791 AC: 120344 AN: 152062 Hom.: 48364 Cov.: 32

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.792 AC: 120466 AN: 152180 Hom.: 48431 Cov.: 32 AF XY: 0.793 AC XY: 58988 AN XY: 74400

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.763

Alfa AF: 0.752 Hom.: 5092

Bravo AF: 0.799

Asia WGS AF: 0.803 AC: 2791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs248166; hg19: chr5-135292708;