6-32889642-T-A

Position:

• chr6-32889642-T-A

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 0.142 in 152,212 control chromosomes in the GnomAD database, including 1,836 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 0.14 (1836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21562 AN: 152094 Hom.: 1832 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0924

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.142 AC: 21604 AN: 152212 Hom.: 1836 Cov.: 32 AF XY: 0.143 AC XY: 10610 AN XY: 74408

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0924

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.132

Alfa AF: 0.122 Hom.: 203

Bravo AF: 0.141

Asia WGS AF: 0.171 AC: 591 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.68
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: rs10214886; hg19: chr6-32857419;