1-118320046-T-C

Variant names:

• chr1-118320046-T-C
• rs17038164

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 0.265 in 152,068 control chromosomes in the GnomAD database, including 5,529 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 0.27 (5529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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: 0.266 AC: 40359 AN: 151950 Hom.: 5528 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.265 AC: 40372 AN: 152068 Hom.: 5529 Cov.: 32 AF XY: 0.265 AC XY: 19736 AN XY: 74344

African (AFR) AF: 0.281 AC: 11644 AN: 41478

American (AMR) AF: 0.266 AC: 4063 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3472

East Asian (EAS) AF: 0.368 AC: 1900 AN: 5170

South Asian (SAS) AF: 0.314 AC: 1517 AN: 4832

European-Finnish (FIN) AF: 0.233 AC: 2462 AN: 10562

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16913 AN: 67988

Other (OTH) AF: 0.249 AC: 526 AN: 2112

Alfa AF: 0.251 Hom.: 13988

Bravo AF: 0.267

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.79
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs17038164; hg19: chr1-118862669;