chr6-142455927-A-G

Position:

• chr6-142455927-A-G

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 0.391 in 151,906 control chromosomes in the GnomAD database, including 13,091 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 0.39 (13091 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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: 0.391 AC: 59296 AN: 151788 Hom.: 13062 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.391 AC: 59382 AN: 151906 Hom.: 13091 Cov.: 31 AF XY: 0.388 AC XY: 28818 AN XY: 74232

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.420

Alfa AF: 0.326 Hom.: 8147

Bravo AF: 0.405

Asia WGS AF: 0.423 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7776375; hg19: chr6-142777064;