5-103291654-T-G

Variant names:

• chr5-103291654-T-G
• rs187580

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 0.162 in 152,110 control chromosomes in the GnomAD database, including 2,576 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 0.16 (2576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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: 0.162 AC: 24620 AN: 151992 Hom.: 2577 Cov.: 32

Gnomad AFR AF: 0.0403

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.162 AC: 24614 AN: 152110 Hom.: 2576 Cov.: 32 AF XY: 0.159 AC XY: 11809 AN XY: 74340

African (AFR) AF: 0.0402 AC: 1670 AN: 41540

American (AMR) AF: 0.147 AC: 2249 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3464

East Asian (EAS) AF: 0.169 AC: 873 AN: 5178

South Asian (SAS) AF: 0.0887 AC: 428 AN: 4824

European-Finnish (FIN) AF: 0.222 AC: 2341 AN: 10542

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15795 AN: 67976

Other (OTH) AF: 0.164 AC: 346 AN: 2108

Alfa AF: 0.207 Hom.: 1847

Bravo AF: 0.151

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.94
DANN	Benign	0.58
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs187580; hg19: chr5-102627355;