13-23510670-T-C

Position:

• chr13-23510670-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000695562.1(ENSG00000289688):​n.217+5216T>C variant causes a intron, non coding transcript 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: ENST00000695562.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124903135	XR_007063720.1	n.201+5216T>C		intron_variant, non_coding_transcript_variant
LOC124903135	XR_007063721.1	n.201+5216T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000695562.1	n.217+5216T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.279

Alfa AF: 0.283 Hom.: 13022

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6490805; hg19: chr13-24084809;