5-2642319-G-A

Position:

• chr5-2642319-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 0.614 in 152,092 control chromosomes in the GnomAD database, including 29,206 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 0.61 (29206 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

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 (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93386 AN: 151974 Hom.: 29201 Cov.: 33

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.614 AC: 93427 AN: 152092 Hom.: 29206 Cov.: 33 AF XY: 0.613 AC XY: 45540 AN XY: 74338

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.614

Alfa AF: 0.643 Hom.: 3901

Bravo AF: 0.601

Asia WGS AF: 0.524 AC: 1824 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	0.60
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6872448; hg19: chr5-2642433;