chr5-73156792-G-T

Position:

• chr5-73156792-G-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 0.19 in 151,596 control chromosomes in the GnomAD database, including 3,282 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 (3282 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 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: 0.190 AC: 28725 AN: 151482 Hom.: 3267 Cov.: 31

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.190 AC: 28782 AN: 151596 Hom.: 3282 Cov.: 31 AF XY: 0.189 AC XY: 13968 AN XY: 74062

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.166

Alfa AF: 0.166 Hom.: 408

Bravo AF: 0.193

Asia WGS AF: 0.202 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs777847; hg19: chr5-72452619;