rs17038182

Variant names:

• chr1-118325782-G-C
• rs17038182

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 0.252 in 152,016 control chromosomes in the GnomAD database, including 4,999 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 0.25 (4999 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 24 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 (EAS) allele frequency at 95% confidence interval = 0.354 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: 0.252 AC: 38346 AN: 151898 Hom.: 5002 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.252 AC: 38346 AN: 152016 Hom.: 4999 Cov.: 32 AF XY: 0.253 AC XY: 18780 AN XY: 74306

African (AFR) AF: 0.238 AC: 9890 AN: 41474

American (AMR) AF: 0.252 AC: 3845 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1892 AN: 5150

South Asian (SAS) AF: 0.315 AC: 1514 AN: 4812

European-Finnish (FIN) AF: 0.233 AC: 2466 AN: 10576

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16892 AN: 67974

Other (OTH) AF: 0.237 AC: 501 AN: 2112

Alfa AF: 0.257 Hom.: 2850

Bravo AF: 0.251

Asia WGS AF: 0.306 AC: 1063 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.56
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs17038182; hg19: chr1-118868405;