rs2089760

Variant names:

• chr18-7118956-C-T
• rs2089760

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 0.435 in 151,700 control chromosomes in the GnomAD database, including 16,591 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 0.44 (16591 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.603 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: 0.436 AC: 66029 AN: 151580 Hom.: 16595 Cov.: 31

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.435 AC: 66026 AN: 151700 Hom.: 16591 Cov.: 31 AF XY: 0.441 AC XY: 32713 AN XY: 74096

African (AFR) AF: 0.168 AC: 6928 AN: 41344

American (AMR) AF: 0.608 AC: 9265 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1885 AN: 3464

East Asian (EAS) AF: 0.586 AC: 3007 AN: 5132

South Asian (SAS) AF: 0.622 AC: 2992 AN: 4810

European-Finnish (FIN) AF: 0.487 AC: 5113 AN: 10490

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35270 AN: 67920

Other (OTH) AF: 0.489 AC: 1028 AN: 2104

Alfa AF: 0.490 Hom.: 47728

Bravo AF: 0.432

Asia WGS AF: 0.587 AC: 2038 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.80
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2089760; hg19: chr18-7118955;