18-68646835-A-T

Variant names:

• chr18-68646835-A-T
• rs1704734

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.819

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1704734; hg19: chr18-66314072;