chr5-2642319-G-A

Variant names:

• chr5-2642319-G-A
• rs6872448

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;