5-175439088-T-G

Variant names:

• chr5-175439088-T-G
• rs11746641

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 0.178 in 152,174 control chromosomes in the GnomAD database, including 2,543 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 (2543 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.46
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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: 0.178 AC: 27094 AN: 152056 Hom.: 2544 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.178 AC: 27108 AN: 152174 Hom.: 2543 Cov.: 33 AF XY: 0.179 AC XY: 13322 AN XY: 74414

African (AFR) AF: 0.213 AC: 8825 AN: 41516

American (AMR) AF: 0.207 AC: 3156 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3472

East Asian (EAS) AF: 0.188 AC: 969 AN: 5168

South Asian (SAS) AF: 0.154 AC: 741 AN: 4826

European-Finnish (FIN) AF: 0.151 AC: 1598 AN: 10606

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10380 AN: 67992

Other (OTH) AF: 0.186 AC: 393 AN: 2110

Alfa AF: 0.168 Hom.: 9809

Bravo AF: 0.188

Asia WGS AF: 0.145 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.7
DANN	Benign	0.52
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs11746641; hg19: chr5-174866091;