6-32411959-G-A

Position:

• chr6-32411959-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 0.0424 in 152,182 control chromosomes in the GnomAD database, including 276 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 0.042 (276 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32411959G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0424 AC: 6444 AN: 152062 Hom.: 275 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0184

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0424 AC: 6447 AN: 152182 Hom.: 276 Cov.: 32 AF XY: 0.0457 AC XY: 3397 AN XY: 74406

Gnomad4 AFR AF: 0.0533

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0184

Gnomad4 OTH AF: 0.0522

Alfa AF: 0.0205 Hom.: 31

Bravo AF: 0.0397

Asia WGS AF: 0.161 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9405098; hg19: chr6-32379736;