6-153972653-T-C

Position:

• chr6-153972653-T-C

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 0.781 in 152,288 control chromosomes in the GnomAD database, including 46,647 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 0.78 (46647 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

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 (AMR) allele frequency at 95% confidence interval = 0.816 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: 0.781 AC: 118850 AN: 152170 Hom.: 46629 Cov.: 35

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.781 AC: 118913 AN: 152288 Hom.: 46647 Cov.: 35 AF XY: 0.784 AC XY: 58366 AN XY: 74464

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.763

Alfa AF: 0.751 Hom.: 10257

Bravo AF: 0.784

Asia WGS AF: 0.745 AC: 2593 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	3.5
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs484565; hg19: chr6-154293788;