6-32792668-G-T

Position:

• chr6-32792668-G-T

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 0.615 in 151,968 control chromosomes in the GnomAD database, including 28,911 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 0.61 (28911 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

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 (SAS) allele frequency at 95% confidence interval = 0.693 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: 0.615 AC: 93345 AN: 151850 Hom.: 28896 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.615 AC: 93399 AN: 151968 Hom.: 28911 Cov.: 32 AF XY: 0.620 AC XY: 46054 AN XY: 74282

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.613

Alfa AF: 0.545 Hom.: 2364

Bravo AF: 0.606

Asia WGS AF: 0.689 AC: 2394 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	0.023
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2621382; hg19: chr6-32760445;