rs12214039

chr6-31092585-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 0.127 in 152,086 control chromosomes in the GnomAD database, including 1,342 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 0.13 (1342 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19287 AN: 151968 Hom.: 1335 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.127 AC: 19309 AN: 152086 Hom.: 1342 Cov.: 31 AF XY: 0.127 AC XY: 9478 AN XY: 74340

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0865

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0993

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.130

Alfa AF: 0.115 Hom.: 165

Bravo AF: 0.130

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.7
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: rs12214039; hg19: chr6-31060362;