5-151020073-T-C

Position:

• chr5-151020073-T-C

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 0.149 in 152,198 control chromosomes in the GnomAD database, including 1,798 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 (1798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22667 AN: 152078 Hom.: 1794 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.149 AC: 22697 AN: 152198 Hom.: 1798 Cov.: 32 AF XY: 0.146 AC XY: 10852 AN XY: 74428

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.0952

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.136

Alfa AF: 0.132 Hom.: 1585

Bravo AF: 0.149

Asia WGS AF: 0.139 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8177406; hg19: chr5-150399634;