6-12196980-C-A

Position:

• chr6-12196980-C-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 0.147 in 152,070 control chromosomes in the GnomAD database, including 2,009 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 0.15 (2009 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12196980C>A		intergenic_region
HIVEP1	XR_007059258.1	n.7531-2241C>A		intron_variant
HIVEP1	XR_007059259.1	n.6799-2241C>A		intron_variant
HIVEP1	XR_007059260.1	n.6741-2241C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22285 AN: 151952 Hom.: 2013 Cov.: 31

Gnomad AFR AF: 0.0588

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.147 AC: 22284 AN: 152070 Hom.: 2009 Cov.: 31 AF XY: 0.144 AC XY: 10719 AN XY: 74354

Gnomad4 AFR AF: 0.0589

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0310

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.173

Alfa AF: 0.197 Hom.: 3663

Bravo AF: 0.141

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.033
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1040994; hg19: chr6-12197213;