rs17079650

Variant names:

• chr13-33724362-T-C
• rs17079650
• ENST00000731018.1:n.194+23967T>C

Variant summary

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

The ENST00000731018.1(ENSG00000295576):​n.194+23967T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 152,052 control chromosomes in the GnomAD database, including 1,003 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 0.078 (1003 hom., cov: 32)
• Consequence: ENSG00000295576 ENST00000731018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 1 publications found

Genes affected

ENSG00000295576 (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 = 0.239 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
ENSG00000295576	ENST00000731018.1	n.194+23967T>C		intron_variant	Intron 1 of 1
ENSG00000288767	ENST00000731141.1	n.51-37471T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11790 AN: 151934 Hom.: 996 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0732

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0778 AC: 11833 AN: 152052 Hom.: 1003 Cov.: 32 AF XY: 0.0792 AC XY: 5889 AN XY: 74340

African (AFR) AF: 0.193 AC: 7991 AN: 41452

American (AMR) AF: 0.0735 AC: 1123 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3466

East Asian (EAS) AF: 0.250 AC: 1290 AN: 5158

South Asian (SAS) AF: 0.0505 AC: 244 AN: 4830

European-Finnish (FIN) AF: 0.0228 AC: 241 AN: 10548

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0110 AC: 750 AN: 68002

Other (OTH) AF: 0.0643 AC: 136 AN: 2116

Alfa AF: 0.0514 Hom.: 78

Bravo AF: 0.0887

Asia WGS AF: 0.175 AC: 605 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs17079650; hg19: chr13-34298499;