rs17839277

Variant names:

• chr5-18021998-G-A
• rs17839277

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 0.046 in 152,066 control chromosomes in the GnomAD database, including 197 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 0.046 (197 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0694 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: 0.0460 AC: 6996 AN: 151948 Hom.: 196 Cov.: 31

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.0366

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0402

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0555

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

GnomAD4 genome AF: 0.0460 AC: 6995 AN: 152066 Hom.: 197 Cov.: 31 AF XY: 0.0466 AC XY: 3461 AN XY: 74332

African (AFR) AF: 0.0715 AC: 2966 AN: 41468

American (AMR) AF: 0.0367 AC: 560 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3470

East Asian (EAS) AF: 0.0405 AC: 208 AN: 5138

South Asian (SAS) AF: 0.0643 AC: 310 AN: 4818

European-Finnish (FIN) AF: 0.0320 AC: 339 AN: 10588

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0326 AC: 2219 AN: 67992

Other (OTH) AF: 0.0549 AC: 116 AN: 2112

Alfa AF: 0.0390 Hom.: 162

Bravo AF: 0.0476

Asia WGS AF: 0.0530 AC: 183 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	4.5
DANN	Benign	0.60
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs17839277; hg19: chr5-18022107;