5-50340488-T-C

Variant names:

• chr5-50340488-T-C
• rs13154900

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 0.111 in 151,832 control chromosomes in the GnomAD database, including 1,110 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 0.11 (1110 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 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: 0.111 AC: 16850 AN: 151716 Hom.: 1110 Cov.: 32

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.111 AC: 16861 AN: 151832 Hom.: 1110 Cov.: 32 AF XY: 0.112 AC XY: 8309 AN XY: 74172

African (AFR) AF: 0.0522 AC: 2165 AN: 41474

American (AMR) AF: 0.121 AC: 1845 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 380 AN: 3462

East Asian (EAS) AF: 0.164 AC: 843 AN: 5150

South Asian (SAS) AF: 0.149 AC: 715 AN: 4810

European-Finnish (FIN) AF: 0.134 AC: 1418 AN: 10552

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9213 AN: 67854

Other (OTH) AF: 0.110 AC: 231 AN: 2102

Alfa AF: 0.110 Hom.: 129

Bravo AF: 0.107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.78
DANN	Benign	0.40
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs13154900; hg19: chr5-49636322;