rs1518108

Variant names:

• chr1-206869829-C-T
• rs1518108

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 0.463 in 151,668 control chromosomes in the GnomAD database, including 16,850 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 0.46 (16850 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 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: 0.463 AC: 70135 AN: 151548 Hom.: 16830 Cov.: 30

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.463 AC: 70209 AN: 151668 Hom.: 16850 Cov.: 30 AF XY: 0.454 AC XY: 33639 AN XY: 74102

African (AFR) AF: 0.567 AC: 23387 AN: 41252

American (AMR) AF: 0.457 AC: 6964 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1623 AN: 3460

East Asian (EAS) AF: 0.222 AC: 1148 AN: 5166

South Asian (SAS) AF: 0.232 AC: 1110 AN: 4792

European-Finnish (FIN) AF: 0.372 AC: 3912 AN: 10518

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30478 AN: 67912

Other (OTH) AF: 0.494 AC: 1043 AN: 2110

Alfa AF: 0.465 Hom.: 2453

Bravo AF: 0.475

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.033
DANN	Benign	0.65
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1518108; hg19: chr1-207043174;