1-117543540-T-C

Variant names:

• chr1-117543540-T-C
• rs10489817

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 0.249 in 151,904 control chromosomes in the GnomAD database, including 5,454 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 (5454 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.458 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: 0.249 AC: 37763 AN: 151786 Hom.: 5448 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.249 AC: 37782 AN: 151904 Hom.: 5454 Cov.: 31 AF XY: 0.251 AC XY: 18644 AN XY: 74250

African (AFR) AF: 0.126 AC: 5229 AN: 41484

American (AMR) AF: 0.212 AC: 3228 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2441 AN: 5152

South Asian (SAS) AF: 0.335 AC: 1614 AN: 4820

European-Finnish (FIN) AF: 0.352 AC: 3696 AN: 10490

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

European-Non Finnish (NFE) AF: 0.299 AC: 20337 AN: 67926

Other (OTH) AF: 0.242 AC: 511 AN: 2108

Alfa AF: 0.266 Hom.: 804

Bravo AF: 0.231

Asia WGS AF: 0.408 AC: 1418 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	1.1
DANN	Benign	0.70
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10489817; hg19: chr1-118086162;