rs11748684

Variant names:

• chr5-42288491-C-T
• rs11748684

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 0.0702 in 152,210 control chromosomes in the GnomAD database, including 436 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 0.070 (436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.1 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: 0.0703 AC: 10687 AN: 152092 Hom.: 436 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0705

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0843

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

GnomAD4 genome AF: 0.0702 AC: 10692 AN: 152210 Hom.: 436 Cov.: 32 AF XY: 0.0692 AC XY: 5149 AN XY: 74412

African (AFR) AF: 0.103 AC: 4279 AN: 41534

American (AMR) AF: 0.0550 AC: 841 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5178

South Asian (SAS) AF: 0.0701 AC: 338 AN: 4820

European-Finnish (FIN) AF: 0.0448 AC: 475 AN: 10592

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0622 AC: 4234 AN: 68018

Other (OTH) AF: 0.0825 AC: 174 AN: 2110

Alfa AF: 0.0739 Hom.: 231

Bravo AF: 0.0723

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.88
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11748684; hg19: chr5-42288593;