rs6872448

Variant names:

• chr5-2642319-G-A
• rs6872448

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 0.614 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.532 AC: 22084 AN: 41506

American (AMR) AF: 0.569 AC: 8705 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2407 AN: 3472

East Asian (EAS) AF: 0.414 AC: 2127 AN: 5140

South Asian (SAS) AF: 0.612 AC: 2948 AN: 4814

European-Finnish (FIN) AF: 0.669 AC: 7074 AN: 10572

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46018 AN: 67978

Other (OTH) AF: 0.614 AC: 1297 AN: 2112

Alfa AF: 0.638 Hom.: 4003

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
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs6872448; hg19: chr5-2642433;