chr5-148821753-T-A

Variant names:

• chr5-148821753-T-A
• rs11959615

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 0.596 in 152,036 control chromosomes in the GnomAD database, including 27,380 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 0.60 (27380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 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: 0.596 AC: 90487 AN: 151918 Hom.: 27362 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.596 AC: 90551 AN: 152036 Hom.: 27380 Cov.: 32 AF XY: 0.603 AC XY: 44823 AN XY: 74294

African (AFR) AF: 0.561 AC: 23267 AN: 41452

American (AMR) AF: 0.707 AC: 10806 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2075 AN: 3470

East Asian (EAS) AF: 0.746 AC: 3851 AN: 5164

South Asian (SAS) AF: 0.739 AC: 3571 AN: 4830

European-Finnish (FIN) AF: 0.633 AC: 6670 AN: 10536

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38279 AN: 67996

Other (OTH) AF: 0.627 AC: 1324 AN: 2110

Alfa AF: 0.575 Hom.: 3168

Bravo AF: 0.596

Asia WGS AF: 0.747 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs11959615; hg19: chr5-148201316;