chr18-7386870-G-T

Variant names:

• chr18-7386870-G-T
• rs16951664

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 0.474 in 151,852 control chromosomes in the GnomAD database, including 17,309 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 0.47 (17309 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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: 0.474 AC: 71914 AN: 151734 Hom.: 17300 Cov.: 30

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.474 AC: 71962 AN: 151852 Hom.: 17309 Cov.: 30 AF XY: 0.474 AC XY: 35151 AN XY: 74186

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.506

Alfa AF: 0.507 Hom.: 26287

Bravo AF: 0.472

Asia WGS AF: 0.475 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16951664; hg19: chr18-7386868;