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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.791 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

African (AFR) AF: 0.943 AC: 39162 AN: 41542

American (AMR) AF: 0.766 AC: 11715 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2592 AN: 3472

East Asian (EAS) AF: 0.786 AC: 4051 AN: 5156

South Asian (SAS) AF: 0.813 AC: 3921 AN: 4820

European-Finnish (FIN) AF: 0.753 AC: 7978 AN: 10590

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.714 AC: 48515 AN: 67994

Other (OTH) AF: 0.763 AC: 1614 AN: 2116

Alfa AF: 0.747 Hom.: 10127

Bravo AF: 0.799

Asia WGS AF: 0.803 AC: 2791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.22
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs248166; hg19: chr5-135292708;