rs719191

Variant names:

• chr5-120146758-G-A
• rs719191

Your query was ambiguous. Multiple possible variants found:

• chr5-120146758-G-A
• chr5-120146758-G-C

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 0.335 in 152,068 control chromosomes in the GnomAD database, including 14,105 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 0.34 (14105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

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 = 0.757 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: 0.335 AC: 50912 AN: 151950 Hom.: 14064 Cov.: 32

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.335 AC: 51005 AN: 152068 Hom.: 14105 Cov.: 32 AF XY: 0.334 AC XY: 24798 AN XY: 74348

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.286

Alfa AF: 0.137 Hom.: 408

Bravo AF: 0.355

Asia WGS AF: 0.342 AC: 1189 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	4.3
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: rs719191; hg19: chr5-119482453;