rs17818837

Variant names:

• chr15-54839085-G-A
• rs17818837

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 0.157 in 151,990 control chromosomes in the GnomAD database, including 2,066 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 0.16 (2066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23836 AN: 151872 Hom.: 2063 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.157 AC: 23846 AN: 151990 Hom.: 2066 Cov.: 32 AF XY: 0.157 AC XY: 11640 AN XY: 74308

African (AFR) AF: 0.127 AC: 5239 AN: 41384

American (AMR) AF: 0.133 AC: 2028 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3470

East Asian (EAS) AF: 0.0373 AC: 193 AN: 5176

South Asian (SAS) AF: 0.133 AC: 642 AN: 4818

European-Finnish (FIN) AF: 0.208 AC: 2203 AN: 10566

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12399 AN: 68004

Other (OTH) AF: 0.169 AC: 356 AN: 2106

Alfa AF: 0.170 Hom.: 1185

Bravo AF: 0.150

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.19
DANN	Benign	0.55
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs17818837; hg19: chr15-55131283;