chr5-1168929-G-T

Variant names:

• chr5-1168929-G-T
• rs7719062

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 0.115 in 152,076 control chromosomes in the GnomAD database, including 1,216 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 (1216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.215 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: 0.114 AC: 17391 AN: 151958 Hom.: 1210 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0545

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.0926

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.115 AC: 17421 AN: 152076 Hom.: 1216 Cov.: 32 AF XY: 0.116 AC XY: 8633 AN XY: 74336

African (AFR) AF: 0.119 AC: 4921 AN: 41468

American (AMR) AF: 0.221 AC: 3382 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 689 AN: 3472

East Asian (EAS) AF: 0.0990 AC: 511 AN: 5162

South Asian (SAS) AF: 0.119 AC: 575 AN: 4822

European-Finnish (FIN) AF: 0.0545 AC: 576 AN: 10566

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.0926 AC: 6297 AN: 67992

Other (OTH) AF: 0.140 AC: 296 AN: 2114

Alfa AF: 0.114 Hom.: 1891

Bravo AF: 0.129

Asia WGS AF: 0.122 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs7719062; hg19: chr5-1169044;