chr5-11929801-G-T

Variant names:

• chr5-11929801-G-T
• rs6884647

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 0.496 in 152,048 control chromosomes in the GnomAD database, including 19,807 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 0.50 (19807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 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: 0.495 AC: 75261 AN: 151930 Hom.: 19766 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.496 AC: 75359 AN: 152048 Hom.: 19807 Cov.: 32 AF XY: 0.500 AC XY: 37124 AN XY: 74320

African (AFR) AF: 0.631 AC: 26165 AN: 41472

American (AMR) AF: 0.495 AC: 7562 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1393 AN: 3468

East Asian (EAS) AF: 0.826 AC: 4264 AN: 5162

South Asian (SAS) AF: 0.601 AC: 2897 AN: 4818

European-Finnish (FIN) AF: 0.379 AC: 4002 AN: 10562

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.404 AC: 27447 AN: 67986

Other (OTH) AF: 0.466 AC: 982 AN: 2108

Alfa AF: 0.433 Hom.: 24031

Bravo AF: 0.513

Asia WGS AF: 0.688 AC: 2388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.18
DANN	Benign	0.50
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs6884647; hg19: chr5-11929913;