chr5-119433779-A-T

Variant names:

• chr5-119433779-A-T
• rs384346

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 152,248 control chromosomes in the GnomAD database, including 1,278 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 0.12 (1278 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 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: 0.115 AC: 17517 AN: 152132 Hom.: 1273 Cov.: 33

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.115 AC: 17521 AN: 152248 Hom.: 1278 Cov.: 33 AF XY: 0.120 AC XY: 8959 AN XY: 74434

African (AFR) AF: 0.0280 AC: 1163 AN: 41578

American (AMR) AF: 0.146 AC: 2232 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 371 AN: 3468

East Asian (EAS) AF: 0.0700 AC: 362 AN: 5172

South Asian (SAS) AF: 0.225 AC: 1085 AN: 4824

European-Finnish (FIN) AF: 0.197 AC: 2089 AN: 10588

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9843 AN: 68010

Other (OTH) AF: 0.114 AC: 240 AN: 2114

Alfa AF: 0.132 Hom.: 210

Bravo AF: 0.102

Asia WGS AF: 0.175 AC: 611 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	6.2
DANN	Benign	0.28
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs384346; hg19: chr5-118769474; COSMIC: COSV60187223;