6-141466657-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 0.316 in 152,006 control chromosomes in the GnomAD database, including 7,821 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 0.32 (7821 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 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: 0.316 AC: 47988 AN: 151888 Hom.: 7811 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.316 AC: 48030 AN: 152006 Hom.: 7821 Cov.: 32 AF XY: 0.319 AC XY: 23715 AN XY: 74310

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.350

Alfa AF: 0.327 Hom.: 8124

Bravo AF: 0.318

Asia WGS AF: 0.389 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.5
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4386830; hg19: chr6-141787794;