6-32687441-T-G

Position:

• chr6-32687441-T-G

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 0.25 in 151,900 control chromosomes in the GnomAD database, including 5,089 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 0.25 (5089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.364 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: 0.250 AC: 37993 AN: 151782 Hom.: 5084 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.250 AC: 38027 AN: 151900 Hom.: 5089 Cov.: 32 AF XY: 0.256 AC XY: 19027 AN XY: 74238

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.266

Alfa AF: 0.263 Hom.: 2939

Bravo AF: 0.262

Asia WGS AF: 0.280 AC: 968 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2856683; hg19: chr6-32655218;