chr5-138471098-A-G

Variant names:

• chr5-138471098-A-G
• rs2051861

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0167 in 151,268 control chromosomes in the GnomAD database, including 24 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 0.017 (24 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0167 (2526/151268) while in subpopulation AFR AF = 0.0204 (840/41162). AF 95% confidence interval is 0.0193. There are 24 homozygotes in GnomAd4. There are 1234 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 24 gene

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: 0.0167 AC: 2522 AN: 151152 Hom.: 24 Cov.: 32

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0122

Gnomad ASJ AF: 0.0359

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0159

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

GnomAD4 genome AF: 0.0167 AC: 2526 AN: 151268 Hom.: 24 Cov.: 32 AF XY: 0.0167 AC XY: 1234 AN XY: 73880

African (AFR) AF: 0.0204 AC: 840 AN: 41162

American (AMR) AF: 0.0122 AC: 185 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.0359 AC: 124 AN: 3458

East Asian (EAS) AF: 0.00 AC: 0 AN: 5118

South Asian (SAS) AF: 0.0193 AC: 92 AN: 4774

European-Finnish (FIN) AF: 0.0127 AC: 133 AN: 10464

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0164 AC: 1112 AN: 67794

Other (OTH) AF: 0.0157 AC: 33 AN: 2100

Alfa AF: 0.0178 Hom.: 12

Bravo AF: 0.0169

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	6.7
DANN	Benign	0.88
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2051861; hg19: chr5-137806787;