rs2860804

Variant names:

• chr5-163838299-G-A
• rs2860804

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 0.307 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

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 (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

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.327

Alfa AF: 0.252 Hom.: 2474

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

Splicing

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

Publications

LitVar

Other links and lift over

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