rs2860804

Variant names:

• chr5-163838299-G-A
• rs2860804

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 0.307 in 151,862 control chromosomes in the GnomAD database, including 7,977 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 0.31 (7977 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.828
• Publications: 1 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 = 0.464 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: 0.307 AC: 46640 AN: 151742 Hom.: 7969 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.307 AC: 46678 AN: 151862 Hom.: 7977 Cov.: 32 AF XY: 0.307 AC XY: 22742 AN XY: 74188

African (AFR) AF: 0.470 AC: 19462 AN: 41422

American (AMR) AF: 0.296 AC: 4518 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1073 AN: 3464

East Asian (EAS) AF: 0.249 AC: 1277 AN: 5136

South Asian (SAS) AF: 0.155 AC: 746 AN: 4798

European-Finnish (FIN) AF: 0.244 AC: 2571 AN: 10558

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16070 AN: 67932

Other (OTH) AF: 0.327 AC: 689 AN: 2104

Alfa AF: 0.260 Hom.: 9203

Bravo AF: 0.322

Asia WGS AF: 0.202 AC: 705 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	7.5
DANN	Benign	0.19
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs2860804; hg19: chr5-163265305; COSMIC: COSV60227055;