5-15022003-G-T

Variant names:

• chr5-15022003-G-T
• rs7727670

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 0.18 in 152,006 control chromosomes in the GnomAD database, including 2,565 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 0.18 (2565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 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: 0.180 AC: 27337 AN: 151890 Hom.: 2565 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.180 AC: 27353 AN: 152006 Hom.: 2565 Cov.: 32 AF XY: 0.180 AC XY: 13392 AN XY: 74288

African (AFR) AF: 0.185 AC: 7648 AN: 41452

American (AMR) AF: 0.162 AC: 2470 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3472

East Asian (EAS) AF: 0.258 AC: 1334 AN: 5162

South Asian (SAS) AF: 0.169 AC: 814 AN: 4806

European-Finnish (FIN) AF: 0.200 AC: 2113 AN: 10564

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.169 AC: 11487 AN: 67970

Other (OTH) AF: 0.206 AC: 436 AN: 2114

Alfa AF: 0.170 Hom.: 4442

Bravo AF: 0.180

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.062
DANN	Benign	0.37
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7727670; hg19: chr5-15022112;