chr6-18114889-C-T

Position:

• chr6-18114889-C-T

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 0.0513 in 152,160 control chromosomes in the GnomAD database, including 284 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 0.051 (284 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0513 AC: 7797 AN: 152042 Hom.: 281 Cov.: 32

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0520

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0513 AC: 7805 AN: 152160 Hom.: 284 Cov.: 32 AF XY: 0.0524 AC XY: 3900 AN XY: 74378

Gnomad4 AFR AF: 0.0150

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0508

Gnomad4 FIN AF: 0.0452

Gnomad4 NFE AF: 0.0520

Gnomad4 OTH AF: 0.0541

Alfa AF: 0.0556 Hom.: 410

Bravo AF: 0.0556

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
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: rs12524744; hg19: chr6-18115120;