5-73156792-G-T

Variant names:

• chr5-73156792-G-T
• rs777847

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 0.19 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.313 AC: 12932 AN: 41278

American (AMR) AF: 0.132 AC: 2015 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3464

East Asian (EAS) AF: 0.255 AC: 1314 AN: 5148

South Asian (SAS) AF: 0.166 AC: 799 AN: 4800

European-Finnish (FIN) AF: 0.148 AC: 1556 AN: 10488

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9253 AN: 67882

Other (OTH) AF: 0.166 AC: 349 AN: 2106

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs777847; hg19: chr5-72452619;