6-32139154-C-T

Variant names:

• chr6-32139154-C-T
• rs7383258

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 0.0525 in 151,914 control chromosomes in the GnomAD database, including 287 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 0.052 (287 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0967 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: 0.0525 AC: 7967 AN: 151796 Hom.: 287 Cov.: 30

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00265

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0412

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0525 AC: 7974 AN: 151914 Hom.: 287 Cov.: 30 AF XY: 0.0493 AC XY: 3661 AN XY: 74272

Gnomad4 AFR AF: 0.0992

Gnomad4 AMR AF: 0.0527

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.00265

Gnomad4 NFE AF: 0.0412

Gnomad4 OTH AF: 0.0529

Alfa AF: 0.0346 Hom.: 64

Bravo AF: 0.0601

Asia WGS AF: 0.00520 AC: 18 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7383258; hg19: chr6-32106931;