rs828199

Variant names:

• chr13-90718584-T-C
• rs828199
• ENST00000741517.1:n.396T>C

Variant summary

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

The ENST00000741517.1(ENSG00000296744):​n.396T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.97 in 152,120 control chromosomes in the GnomAD database, including 71,714 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 0.97 (71714 hom., cov: 31)
• Consequence: ENSG00000296744 ENST00000741517.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680
• Publications: 3 publications found

Genes affected

ENSG00000296744 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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
ENSG00000296744	ENST00000741517.1	n.396T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000296744	ENST00000741518.1	n.582T>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000296712	ENST00000741265.1	n.292+2320A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.970 AC: 147418 AN: 152002 Hom.: 71658 Cov.: 31

Gnomad AFR AF: 0.895

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.990

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.994

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.972

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

GnomAD4 genome AF: 0.970 AC: 147532 AN: 152120 Hom.: 71714 Cov.: 31 AF XY: 0.971 AC XY: 72223 AN XY: 74366

African (AFR) AF: 0.895 AC: 37149 AN: 41510

American (AMR) AF: 0.990 AC: 15118 AN: 15266

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3470 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5158 AN: 5158

South Asian (SAS) AF: 1.00 AC: 4816 AN: 4816

European-Finnish (FIN) AF: 1.00 AC: 10624 AN: 10624

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67940 AN: 67958

Other (OTH) AF: 0.972 AC: 2053 AN: 2112

Alfa AF: 0.961 Hom.: 31591

Bravo AF: 0.966

Asia WGS AF: 0.998 AC: 3470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs828199; hg19: chr13-91370838;