chr13-23963862-A-G

Position:

• chr13-23963862-A-G

Variant summary

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

The ENST00000655811.1(ENSG00000287530):​n.258-4778A>G 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 0.323 in 152,078 control chromosomes in the GnomAD database, including 8,320 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 0.32 (8320 hom., cov: 33)
• Consequence: ENST00000655811.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370115	XR_941753.2	n.363-540A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000655811.1	n.258-4778A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49019 AN: 151960 Hom.: 8312 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.323 AC: 49064 AN: 152078 Hom.: 8320 Cov.: 33 AF XY: 0.321 AC XY: 23819 AN XY: 74310

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.0602

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.309

Alfa AF: 0.359 Hom.: 1283

Bravo AF: 0.306

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7330124; hg19: chr13-24538001;