rs2391777

Positions:

• chr13-109605896-G-A

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.759-34738C>T 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 0.447 in 152,136 control chromosomes in the GnomAD database, including 15,713 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 0.45 (15713 hom., cov: 33)
• Consequence: ENST00000650264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676

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 (SAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903210	XR_007063870.1	n.940+313C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650264.1	n.759-34738C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67882 AN: 152018 Hom.: 15691 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.447 AC: 67949 AN: 152136 Hom.: 15713 Cov.: 33 AF XY: 0.450 AC XY: 33477 AN XY: 74382

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.434

Alfa AF: 0.423 Hom.: 2368

Bravo AF: 0.456

Asia WGS AF: 0.531 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.62
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2391777; hg19: chr13-110258243;