chr6-32427688-T-G

Variant names:

• chr6-32427688-T-G
• rs1894552

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 0.135 in 152,198 control chromosomes in the GnomAD database, including 1,642 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 (1642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 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: 0.135 AC: 20545 AN: 152080 Hom.: 1642 Cov.: 32

Gnomad AFR AF: 0.0658

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0932

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.135 AC: 20552 AN: 152198 Hom.: 1642 Cov.: 32 AF XY: 0.133 AC XY: 9932 AN XY: 74412

Gnomad4 AFR AF: 0.0661

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.0928

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0784 Hom.: 129

Bravo AF: 0.126

Asia WGS AF: 0.127 AC: 439 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1894552; hg19: chr6-32395465;