chr13-23510670-T-C

Variant names:

• chr13-23510670-T-C
• rs6490805
• ENST00000695562.2:n.261+5216T>C

Variant summary

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

The ENST00000695562.2(ENSG00000289688):​n.261+5216T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,082 control chromosomes in the GnomAD database, including 6,083 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 0.28 (6083 hom., cov: 32)
• Consequence: ENSG00000289688 ENST00000695562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 8 publications found

Genes affected

ENSG00000289688 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903135	XR_007063720.1	n.201+5216T>C		intron_variant	Intron 1 of 2
LOC124903135	XR_007063721.1	n.201+5216T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289688	ENST00000695562.2	n.261+5216T>C		intron_variant	Intron 1 of 1
ENSG00000298148	ENST00000753319.1	n.261-5117A>G		intron_variant	Intron 2 of 2
ENSG00000289688	ENST00000753448.1	n.182+5216T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42076 AN: 151964 Hom.: 6085 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.277 AC: 42094 AN: 152082 Hom.: 6083 Cov.: 32 AF XY: 0.280 AC XY: 20830 AN XY: 74348

African (AFR) AF: 0.263 AC: 10911 AN: 41494

American (AMR) AF: 0.307 AC: 4694 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3472

East Asian (EAS) AF: 0.132 AC: 682 AN: 5172

South Asian (SAS) AF: 0.144 AC: 697 AN: 4826

European-Finnish (FIN) AF: 0.372 AC: 3925 AN: 10556

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19602 AN: 67962

Other (OTH) AF: 0.279 AC: 589 AN: 2110

Alfa AF: 0.280 Hom.: 26399

Bravo AF: 0.274

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6490805; hg19: chr13-24084809;