1-118590986-T-C

Variant names:

• chr1-118590986-T-C
• rs4329498

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 0.357 in 152,078 control chromosomes in the GnomAD database, including 11,461 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 0.36 (11461 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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: 0.358 AC: 54346 AN: 151960 Hom.: 11462 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.357 AC: 54340 AN: 152078 Hom.: 11461 Cov.: 32 AF XY: 0.353 AC XY: 26254 AN XY: 74338

African (AFR) AF: 0.152 AC: 6308 AN: 41514

American (AMR) AF: 0.367 AC: 5613 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1873 AN: 3470

East Asian (EAS) AF: 0.0898 AC: 464 AN: 5168

South Asian (SAS) AF: 0.400 AC: 1931 AN: 4828

European-Finnish (FIN) AF: 0.386 AC: 4070 AN: 10552

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32567 AN: 67950

Other (OTH) AF: 0.405 AC: 856 AN: 2114

Alfa AF: 0.449 Hom.: 27284

Bravo AF: 0.344

Asia WGS AF: 0.240 AC: 835 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.0
DANN	Benign	0.71
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs4329498; hg19: chr1-119133609;