rs248364

Variant names:

• chr5-161259626-A-G
• rs248364

Your query was ambiguous. Multiple possible variants found:

• chr5-161259626-A-G
• chr5-161259626-A-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 0.583 in 151,962 control chromosomes in the GnomAD database, including 27,600 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 0.58 (27600 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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: 0.583 AC: 88523 AN: 151844 Hom.: 27601 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.583 AC: 88554 AN: 151962 Hom.: 27600 Cov.: 31 AF XY: 0.582 AC XY: 43200 AN XY: 74268

African (AFR) AF: 0.353 AC: 14636 AN: 41446

American (AMR) AF: 0.520 AC: 7943 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2198 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3776 AN: 5124

South Asian (SAS) AF: 0.664 AC: 3202 AN: 4820

European-Finnish (FIN) AF: 0.656 AC: 6914 AN: 10546

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47725 AN: 67962

Other (OTH) AF: 0.585 AC: 1235 AN: 2112

Alfa AF: 0.620 Hom.: 3991

Bravo AF: 0.561

Asia WGS AF: 0.696 AC: 2420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.84
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs248364; hg19: chr5-160686633;