18-68646835-A-T

Variant names:

• chr18-68646835-A-T
• rs1704734

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 0.793 in 152,058 control chromosomes in the GnomAD database, including 48,453 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 0.79 (48453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.882 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: 0.793 AC: 120485 AN: 151938 Hom.: 48446 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.793 AC: 120532 AN: 152058 Hom.: 48453 Cov.: 32 AF XY: 0.797 AC XY: 59266 AN XY: 74336

African (AFR) AF: 0.654 AC: 27114 AN: 41470

American (AMR) AF: 0.792 AC: 12081 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3043 AN: 3468

East Asian (EAS) AF: 0.845 AC: 4374 AN: 5174

South Asian (SAS) AF: 0.904 AC: 4362 AN: 4824

European-Finnish (FIN) AF: 0.882 AC: 9339 AN: 10590

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57360 AN: 67956

Other (OTH) AF: 0.819 AC: 1731 AN: 2114

Alfa AF: 0.813 Hom.: 6287

Bravo AF: 0.779

Asia WGS AF: 0.865 AC: 3006 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.38
DANN	Benign	0.63
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1704734; hg19: chr18-66314072;