6-32477823-G-A

Position:

• chr6-32477823-G-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 0.29 in 152,072 control chromosomes in the GnomAD database, including 6,802 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 0.29 (6802 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975

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 (AMR) allele frequency at 95% confidence interval = 0.35 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: 0.290 AC: 44140 AN: 151954 Hom.: 6801 Cov.: 35

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.290 AC: 44167 AN: 152072 Hom.: 6802 Cov.: 35 AF XY: 0.286 AC XY: 21288 AN XY: 74320

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.304

Alfa AF: 0.0964 Hom.: 113

Bravo AF: 0.307

Asia WGS AF: 0.251 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
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: rs9405112; hg19: chr6-32445600;