6-32243540-C-T

Variant names:

• chr6-32243540-C-T
• rs411326

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.37 (5620 hom., cov: 14)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 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: 0.372 AC: 35899 AN: 96436 Hom.: 5611 Cov.: 14

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.372 AC: 35952 AN: 96546 Hom.: 5620 Cov.: 14 AF XY: 0.380 AC XY: 17465 AN XY: 45934

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.375

Alfa AF: 0.244 Hom.: 3583

Bravo AF: 0.295

Asia WGS AF: 0.343 AC: 1185 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs411326; hg19: chr6-32211317; COSMIC: COSV53487406;