6-32411324-T-C

Variant names:

• chr6-32411324-T-C
• rs5007259

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 0.554 in 151,960 control chromosomes in the GnomAD database, including 23,704 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 0.55 (23704 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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: 0.554 AC: 84176 AN: 151842 Hom.: 23690 Cov.: 31

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.554 AC: 84230 AN: 151960 Hom.: 23704 Cov.: 31 AF XY: 0.559 AC XY: 41474 AN XY: 74256

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.566

Alfa AF: 0.523 Hom.: 11355

Bravo AF: 0.563

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.78
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5007259; hg19: chr6-32379101;