rs3997872

Positions:

• chr6-32612840-T-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 0.139 in 152,224 control chromosomes in the GnomAD database, including 1,676 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 (1676 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32612840T>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21133 AN: 152106 Hom.: 1674 Cov.: 33

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0777

Gnomad SAS AF: 0.0730

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.139 AC: 21158 AN: 152224 Hom.: 1676 Cov.: 33 AF XY: 0.138 AC XY: 10235 AN XY: 74426

Gnomad4 AFR AF: 0.0898

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0781

Gnomad4 SAS AF: 0.0731

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.125

Alfa AF: 0.146 Hom.: 224

Bravo AF: 0.147

Asia WGS AF: 0.0770 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3997872; hg19: chr6-32580617;