rs17093348

Variant names:

• chr14-60207772-G-A
• rs17093348
• ENST00000791883.1:n.212+2663C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-60207772-G-A
• chr14-60207772-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000791883.1(ENSG00000303107):​n.212+2663C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0825 in 152,212 control chromosomes in the GnomAD database, including 918 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 0.082 (918 hom., cov: 32)
• Consequence: ENSG00000303107 ENST00000791883.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 1 publications found

Genes affected

ENSG00000303107 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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
ENSG00000303107	ENST00000791883.1	n.212+2663C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12483 AN: 152092 Hom.: 896 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.0999

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0702

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

GnomAD4 genome AF: 0.0825 AC: 12556 AN: 152212 Hom.: 918 Cov.: 32 AF XY: 0.0824 AC XY: 6130 AN XY: 74432

African (AFR) AF: 0.173 AC: 7193 AN: 41516

American (AMR) AF: 0.0579 AC: 885 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0903 AC: 313 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1075 AN: 5162

South Asian (SAS) AF: 0.100 AC: 483 AN: 4830

European-Finnish (FIN) AF: 0.0162 AC: 172 AN: 10610

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0330 AC: 2243 AN: 68016

Other (OTH) AF: 0.0723 AC: 153 AN: 2116

Alfa AF: 0.0478 Hom.: 79

Bravo AF: 0.0883

Asia WGS AF: 0.144 AC: 502 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	0.77
DANN	Benign	0.68
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs17093348; hg19: chr14-60674490;