rs2656989

Variant names:

• chr5-82894900-C-T
• rs2656989

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 0.153 in 152,180 control chromosomes in the GnomAD database, including 2,003 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 0.15 (2003 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 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: 0.153 AC: 23298 AN: 152062 Hom.: 1999 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.153 AC: 23316 AN: 152180 Hom.: 2003 Cov.: 33 AF XY: 0.158 AC XY: 11783 AN XY: 74414

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.153

Alfa AF: 0.157 Hom.: 246

Bravo AF: 0.148

Asia WGS AF: 0.249 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	7.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2656989; hg19: chr5-82190719; COSMIC: COSV60160527;