5-150157783-T-C

Variant names:

• chr5-150157783-T-C
• rs3756314

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 0.191 in 152,156 control chromosomes in the GnomAD database, including 4,002 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 0.19 (4002 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 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: 0.191 AC: 29037 AN: 152038 Hom.: 3999 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.0991

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.191 AC: 29066 AN: 152156 Hom.: 4002 Cov.: 33 AF XY: 0.192 AC XY: 14247 AN XY: 74388

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.0991

Gnomad4 OTH AF: 0.175

Alfa AF: 0.168 Hom.: 312

Bravo AF: 0.199

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3756314; hg19: chr5-149537346;