6-122368255-A-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 0.404 in 152,098 control chromosomes in the GnomAD database, including 13,142 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 0.40 (13142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 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: 0.404 AC: 61413 AN: 151980 Hom.: 13142 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.404 AC: 61429 AN: 152098 Hom.: 13142 Cov.: 32 AF XY: 0.399 AC XY: 29702 AN XY: 74354

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.424

Alfa AF: 0.438 Hom.: 1885

Bravo AF: 0.397

Asia WGS AF: 0.354 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.44
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13204990; hg19: chr6-122689400;