rs6898653

Variant names:

• chr5-116639960-A-G
• rs6898653

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 0.258 in 152,028 control chromosomes in the GnomAD database, including 5,640 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 0.26 (5640 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 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: 0.258 AC: 39144 AN: 151910 Hom.: 5628 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.258 AC: 39189 AN: 152028 Hom.: 5640 Cov.: 32 AF XY: 0.257 AC XY: 19130 AN XY: 74316

African (AFR) AF: 0.396 AC: 16405 AN: 41418

American (AMR) AF: 0.206 AC: 3149 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3470

East Asian (EAS) AF: 0.175 AC: 905 AN: 5172

South Asian (SAS) AF: 0.238 AC: 1149 AN: 4830

European-Finnish (FIN) AF: 0.233 AC: 2467 AN: 10572

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13688 AN: 67972

Other (OTH) AF: 0.247 AC: 522 AN: 2110

Alfa AF: 0.216 Hom.: 14966

Bravo AF: 0.259

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.80
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6898653; hg19: chr5-115975656;