6-32411324-T-C

Variant names:

• chr6-32411324-T-C
• rs5007259

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 41 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.599 AC: 24816 AN: 41416

American (AMR) AF: 0.564 AC: 8621 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2063 AN: 3470

East Asian (EAS) AF: 0.673 AC: 3476 AN: 5166

South Asian (SAS) AF: 0.649 AC: 3126 AN: 4816

European-Finnish (FIN) AF: 0.547 AC: 5760 AN: 10536

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.506 AC: 34423 AN: 67968

Other (OTH) AF: 0.566 AC: 1191 AN: 2104

Alfa AF: 0.528 Hom.: 50276

Bravo AF: 0.563

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.78
DANN	Benign	0.25
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs5007259; hg19: chr6-32379101;