6-122368255-A-T

Variant names:

• chr6-122368255-A-T
• rs13204990

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;