5-131110726-C-T

Variant names:

• chr5-131110726-C-T
• rs7728773

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 0.297 in 152,020 control chromosomes in the GnomAD database, including 7,742 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 0.30 (7742 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 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: 0.297 AC: 45169 AN: 151902 Hom.: 7727 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.297 AC: 45211 AN: 152020 Hom.: 7742 Cov.: 32 AF XY: 0.296 AC XY: 21987 AN XY: 74306

African (AFR) AF: 0.480 AC: 19900 AN: 41430

American (AMR) AF: 0.212 AC: 3245 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1115 AN: 5186

South Asian (SAS) AF: 0.265 AC: 1280 AN: 4824

European-Finnish (FIN) AF: 0.277 AC: 2933 AN: 10576

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15248 AN: 67946

Other (OTH) AF: 0.269 AC: 565 AN: 2104

Alfa AF: 0.248 Hom.: 3056

Bravo AF: 0.296

Asia WGS AF: 0.291 AC: 1012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.96
DANN	Benign	0.43
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs7728773; hg19: chr5-130446419;