chr5-119681605-T-C

Variant names:

• chr5-119681605-T-C
• rs330201

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 0.794 in 152,138 control chromosomes in the GnomAD database, including 48,525 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 0.79 (48525 hom., cov: 32)
• Consequence: LOC348958 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 4 publications found

Genes affected

LOC348958 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC348958		n.119681605T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120701 AN: 152020 Hom.: 48472 Cov.: 32

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.794 AC: 120815 AN: 152138 Hom.: 48525 Cov.: 32 AF XY: 0.788 AC XY: 58624 AN XY: 74388

African (AFR) AF: 0.928 AC: 38530 AN: 41512

American (AMR) AF: 0.724 AC: 11062 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2596 AN: 3470

East Asian (EAS) AF: 0.867 AC: 4492 AN: 5182

South Asian (SAS) AF: 0.745 AC: 3592 AN: 4822

European-Finnish (FIN) AF: 0.667 AC: 7050 AN: 10570

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50845 AN: 67988

Other (OTH) AF: 0.792 AC: 1671 AN: 2110

Alfa AF: 0.761 Hom.: 75156

Bravo AF: 0.804

Asia WGS AF: 0.775 AC: 2695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.4
DANN	Benign	0.57
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs330201; hg19: chr5-119017300;