rs12214039

Variant names:

• chr6-31092585-G-T
• rs12214039

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.175 AC: 7252 AN: 41468

American (AMR) AF: 0.0865 AC: 1320 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3470

East Asian (EAS) AF: 0.170 AC: 878 AN: 5160

South Asian (SAS) AF: 0.129 AC: 620 AN: 4808

European-Finnish (FIN) AF: 0.0993 AC: 1052 AN: 10594

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7146 AN: 68000

Other (OTH) AF: 0.130 AC: 275 AN: 2114

Alfa AF: 0.118 Hom.: 176

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
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs12214039; hg19: chr6-31060362;