18-8894371-C-T

Variant names:

• chr18-8894371-C-T
• rs675935

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 0.354 in 151,956 control chromosomes in the GnomAD database, including 9,758 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 0.35 (9758 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.377 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: 0.354 AC: 53788 AN: 151836 Hom.: 9748 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.354 AC: 53833 AN: 151956 Hom.: 9758 Cov.: 32 AF XY: 0.352 AC XY: 26122 AN XY: 74274

African (AFR) AF: 0.382 AC: 15836 AN: 41414

American (AMR) AF: 0.382 AC: 5839 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1128 AN: 3464

East Asian (EAS) AF: 0.223 AC: 1155 AN: 5174

South Asian (SAS) AF: 0.263 AC: 1265 AN: 4812

European-Finnish (FIN) AF: 0.329 AC: 3470 AN: 10544

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23962 AN: 67958

Other (OTH) AF: 0.337 AC: 713 AN: 2114

Alfa AF: 0.328 Hom.: 3942

Bravo AF: 0.360

Asia WGS AF: 0.239 AC: 829 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.8
DANN	Benign	0.58
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs675935; hg19: chr18-8894369;