5-171754233-T-G

Variant names:

• chr5-171754233-T-G
• rs153750

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 0.705 in 151,240 control chromosomes in the GnomAD database, including 38,494 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 0.71 (38494 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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: 0.705 AC: 106591 AN: 151126 Hom.: 38448 Cov.: 28

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.705 AC: 106691 AN: 151240 Hom.: 38494 Cov.: 28 AF XY: 0.702 AC XY: 51882 AN XY: 73870

African (AFR) AF: 0.876 AC: 36090 AN: 41178

American (AMR) AF: 0.668 AC: 10153 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2023 AN: 3466

East Asian (EAS) AF: 0.595 AC: 3045 AN: 5116

South Asian (SAS) AF: 0.716 AC: 3433 AN: 4798

European-Finnish (FIN) AF: 0.622 AC: 6494 AN: 10436

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.637 AC: 43147 AN: 67748

Other (OTH) AF: 0.674 AC: 1419 AN: 2106

Alfa AF: 0.666 Hom.: 87060

Bravo AF: 0.716

Asia WGS AF: 0.699 AC: 2427 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	8.7
DANN	Benign	0.73
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs153750; hg19: chr5-171181237; COSMIC: COSV68863575;