6-153684478-C-T

Variant names:

• chr6-153684478-C-T
• rs2186140

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 0.497 in 151,922 control chromosomes in the GnomAD database, including 19,234 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 0.50 (19234 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.606 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: 0.497 AC: 75498 AN: 151800 Hom.: 19207 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.497 AC: 75565 AN: 151922 Hom.: 19234 Cov.: 31 AF XY: 0.500 AC XY: 37093 AN XY: 74258

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.528

Alfa AF: 0.456 Hom.: 26762

Bravo AF: 0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2186140; hg19: chr6-154005613;