5-119410415-C-T

Variant names:

• chr5-119410415-C-T
• rs7721752

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 0.727 in 152,086 control chromosomes in the GnomAD database, including 40,752 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 0.73 (40752 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 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: 0.727 AC: 110511 AN: 151968 Hom.: 40716 Cov.: 31

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.727 AC: 110601 AN: 152086 Hom.: 40752 Cov.: 31 AF XY: 0.724 AC XY: 53826 AN XY: 74344

African (AFR) AF: 0.849 AC: 35233 AN: 41498

American (AMR) AF: 0.649 AC: 9917 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2087 AN: 3466

East Asian (EAS) AF: 0.611 AC: 3161 AN: 5172

South Asian (SAS) AF: 0.771 AC: 3718 AN: 4822

European-Finnish (FIN) AF: 0.644 AC: 6805 AN: 10560

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47359 AN: 67974

Other (OTH) AF: 0.705 AC: 1490 AN: 2114

Alfa AF: 0.703 Hom.: 9137

Bravo AF: 0.726

Asia WGS AF: 0.680 AC: 2368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.35
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs7721752; hg19: chr5-118746110;