rs17084857

Variant names:

• chr13-26895631-T-C
• rs17084857
• ENST00000822331.1:n.250-9012T>C

Variant summary

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

The ENST00000822331.1(ENSG00000306970):​n.250-9012T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0922 in 152,232 control chromosomes in the GnomAD database, including 811 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 0.092 (811 hom., cov: 32)
• Consequence: ENSG00000306970 ENST00000822331.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648
• Publications: 4 publications found

Genes affected

ENSG00000306970 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.173 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
ENSG00000306970	ENST00000822331.1	n.250-9012T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0921 AC: 14014 AN: 152114 Hom.: 800 Cov.: 32

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0888

Gnomad OTH AF: 0.0790

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

GnomAD4 genome AF: 0.0922 AC: 14029 AN: 152232 Hom.: 811 Cov.: 32 AF XY: 0.0945 AC XY: 7037 AN XY: 74430

African (AFR) AF: 0.0629 AC: 2614 AN: 41554

American (AMR) AF: 0.164 AC: 2507 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0357 AC: 124 AN: 3470

East Asian (EAS) AF: 0.183 AC: 945 AN: 5172

South Asian (SAS) AF: 0.104 AC: 502 AN: 4826

European-Finnish (FIN) AF: 0.0998 AC: 1059 AN: 10614

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0888 AC: 6037 AN: 67998

Other (OTH) AF: 0.0787 AC: 166 AN: 2110

Alfa AF: 0.0944 Hom.: 352

Bravo AF: 0.0975

Asia WGS AF: 0.172 AC: 596 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	0.84
DANN	Benign	0.55
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs17084857; hg19: chr13-27469768;