17-14657699-T-C

Variant names:

• chr17-14657699-T-C
• rs12940030

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 0.449 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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.797 AC: 33063 AN: 41478

American (AMR) AF: 0.369 AC: 5632 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1251 AN: 3466

East Asian (EAS) AF: 0.563 AC: 2887 AN: 5124

South Asian (SAS) AF: 0.357 AC: 1716 AN: 4810

European-Finnish (FIN) AF: 0.260 AC: 2742 AN: 10542

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.286 AC: 19440 AN: 67904

Other (OTH) AF: 0.422 AC: 891 AN: 2112

Alfa AF: 0.336 Hom.: 40555

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
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs12940030; hg19: chr17-14561016;