chr6-154633286-C-T

Variant names:

• chr6-154633286-C-T
• rs12523822

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 0.349 in 152,018 control chromosomes in the GnomAD database, including 9,419 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 0.35 (9419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 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: 0.348 AC: 52933 AN: 151898 Hom.: 9403 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.349 AC: 52988 AN: 152018 Hom.: 9419 Cov.: 32 AF XY: 0.349 AC XY: 25904 AN XY: 74296

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.362

Alfa AF: 0.305 Hom.: 3876

Bravo AF: 0.347

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.66
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12523822; hg19: chr6-154954420;