chr5-175456049-C-T

Variant names:

• chr5-175456049-C-T
• rs11749035

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 0.153 in 152,014 control chromosomes in the GnomAD database, including 1,839 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 0.15 (1839 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.185 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: 0.153 AC: 23242 AN: 151896 Hom.: 1836 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.153 AC: 23257 AN: 152014 Hom.: 1839 Cov.: 31 AF XY: 0.154 AC XY: 11458 AN XY: 74298

African (AFR) AF: 0.141 AC: 5857 AN: 41430

American (AMR) AF: 0.191 AC: 2920 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3472

East Asian (EAS) AF: 0.177 AC: 918 AN: 5172

South Asian (SAS) AF: 0.139 AC: 669 AN: 4820

European-Finnish (FIN) AF: 0.150 AC: 1579 AN: 10556

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9999 AN: 67962

Other (OTH) AF: 0.169 AC: 356 AN: 2112

Alfa AF: 0.153 Hom.: 3072

Bravo AF: 0.160

Asia WGS AF: 0.135 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs11749035; hg19: chr5-174883052;