rs2505039

Variant names:

• chr6-109984701-C-T
• rs2505039

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 0.592 in 151,860 control chromosomes in the GnomAD database, including 29,308 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 0.59 (29308 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.865 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: 0.592 AC: 89842 AN: 151742 Hom.: 29243 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.592 AC: 89959 AN: 151860 Hom.: 29308 Cov.: 31 AF XY: 0.593 AC XY: 44014 AN XY: 74204

African (AFR) AF: 0.873 AC: 36170 AN: 41444

American (AMR) AF: 0.516 AC: 7869 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3470

East Asian (EAS) AF: 0.829 AC: 4284 AN: 5166

South Asian (SAS) AF: 0.535 AC: 2574 AN: 4810

European-Finnish (FIN) AF: 0.472 AC: 4946 AN: 10484

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.450 AC: 30560 AN: 67904

Other (OTH) AF: 0.583 AC: 1232 AN: 2114

Alfa AF: 0.492 Hom.: 24693

Bravo AF: 0.607

Asia WGS AF: 0.671 AC: 2332 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	0.30
DANN	Benign	0.68
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2505039; hg19: chr6-110305904; COSMIC: COSV51573400;