rs11749035

chr5-175456049-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.169

Alfa AF: 0.148 Hom.: 302

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11749035; hg19: chr5-174883052;