chr13-98065907-T-C

Variant names:

• chr13-98065907-T-C
• rs285028
• ENST00000717002.1:n.493+390A>G

Variant summary

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

The ENST00000717002.1(ENSG00000293659):​n.493+390A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 151,838 control chromosomes in the GnomAD database, including 70,903 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 0.96 (70903 hom., cov: 27)
• Consequence: ENSG00000293659 ENST00000717002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 2 publications found

Genes affected

ENSG00000293659 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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
ENSG00000293659	ENST00000717002.1	n.493+390A>G		intron_variant	Intron 4 of 4
ENSG00000293659	ENST00000717003.1	n.350+1050A>G		intron_variant	Intron 3 of 4
ENSG00000293659	ENST00000717004.1	n.912+390A>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.965 AC: 146409 AN: 151720 Hom.: 70852 Cov.: 27

Gnomad AFR AF: 0.880

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.983

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.978

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

GnomAD4 genome AF: 0.965 AC: 146518 AN: 151838 Hom.: 70903 Cov.: 27 AF XY: 0.965 AC XY: 71623 AN XY: 74204

African (AFR) AF: 0.880 AC: 36350 AN: 41310

American (AMR) AF: 0.983 AC: 15008 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3456 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5132 AN: 5132

South Asian (SAS) AF: 0.999 AC: 4793 AN: 4796

European-Finnish (FIN) AF: 1.00 AC: 10558 AN: 10558

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67961 AN: 68000

Other (OTH) AF: 0.978 AC: 2058 AN: 2104

Alfa AF: 0.983 Hom.: 4780

Bravo AF: 0.960

Asia WGS AF: 0.992 AC: 3449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.80
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs285028; hg19: chr13-98718161;