chr5-151274920-G-T

Variant names:

• chr5-151274920-G-T
• rs7717132

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 0.474 in 152,066 control chromosomes in the GnomAD database, including 18,063 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 0.47 (18063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 14 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 (AFR) allele frequency at 95% confidence interval = 0.615 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: 0.474 AC: 71978 AN: 151948 Hom.: 18040 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.474 AC: 72034 AN: 152066 Hom.: 18063 Cov.: 32 AF XY: 0.476 AC XY: 35362 AN XY: 74330

African (AFR) AF: 0.621 AC: 25794 AN: 41504

American (AMR) AF: 0.543 AC: 8301 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1520 AN: 3472

East Asian (EAS) AF: 0.480 AC: 2485 AN: 5172

South Asian (SAS) AF: 0.545 AC: 2625 AN: 4820

European-Finnish (FIN) AF: 0.335 AC: 3538 AN: 10554

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26371 AN: 67960

Other (OTH) AF: 0.471 AC: 990 AN: 2104

Alfa AF: 0.428 Hom.: 44619

Bravo AF: 0.499

Asia WGS AF: 0.484 AC: 1679 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	2.6
DANN	Benign	0.55
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7717132; hg19: chr5-150654481;