rs12940030

Variant names:

• chr17-14657699-T-C
• rs12940030

Your query was ambiguous. Multiple possible variants found:

• chr17-14657699-T-C
• chr17-14657699-T-G

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 0.449 in 151,896 control chromosomes in the GnomAD database, including 19,079 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 0.45 (19079 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 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: 0.449 AC: 68104 AN: 151782 Hom.: 19043 Cov.: 31

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.449 AC: 68186 AN: 151896 Hom.: 19079 Cov.: 31 AF XY: 0.446 AC XY: 33118 AN XY: 74216

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.422

Alfa AF: 0.317 Hom.: 16492

Bravo AF: 0.476

Asia WGS AF: 0.445 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.7
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12940030; hg19: chr17-14561016;