13-23961849-T-C

Position:

• chr13-23961849-T-C

Variant summary

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

The ENST00000655811.1(ENSG00000287530):​n.257+3111T>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 0.66 in 151,952 control chromosomes in the GnomAD database, including 33,426 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 0.66 (33426 hom., cov: 31)
• Consequence: ENST00000655811.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.592

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370115	XR_941753.2	n.363-2553T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655811.1	n.257+3111T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100195 AN: 151836 Hom.: 33419 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.660 AC: 100230 AN: 151952 Hom.: 33426 Cov.: 31 AF XY: 0.658 AC XY: 48890 AN XY: 74296

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.647

Alfa AF: 0.685 Hom.: 17723

Bravo AF: 0.649

Asia WGS AF: 0.513 AC: 1783 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1886797; hg19: chr13-24535988;