chr5-175432494-C-G

Variant names:

• chr5-175432494-C-G
• rs11742274

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 0.169 in 152,208 control chromosomes in the GnomAD database, including 2,260 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 0.17 (2260 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.197 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: 0.170 AC: 25783 AN: 152090 Hom.: 2259 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.169 AC: 25786 AN: 152208 Hom.: 2260 Cov.: 33 AF XY: 0.170 AC XY: 12681 AN XY: 74410

African (AFR) AF: 0.143 AC: 5955 AN: 41520

American (AMR) AF: 0.203 AC: 3097 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3470

East Asian (EAS) AF: 0.189 AC: 977 AN: 5180

South Asian (SAS) AF: 0.114 AC: 550 AN: 4820

European-Finnish (FIN) AF: 0.185 AC: 1960 AN: 10594

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12237 AN: 68014

Other (OTH) AF: 0.175 AC: 370 AN: 2114

Alfa AF: 0.160 Hom.: 1149

Bravo AF: 0.174

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs11742274; hg19: chr5-174859497;