5-19348755-G-A

Position:

• chr5-19348755-G-A

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 0.405 in 151,718 control chromosomes in the GnomAD database, including 13,147 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 0.40 (13147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61388 AN: 151600 Hom.: 13144 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.405 AC: 61415 AN: 151718 Hom.: 13147 Cov.: 32 AF XY: 0.401 AC XY: 29749 AN XY: 74112

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.401

Alfa AF: 0.452 Hom.: 8915

Bravo AF: 0.404

Asia WGS AF: 0.273 AC: 949 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.40
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2048554; hg19: chr5-19348864;