rs2391777

Variant names:

• chr13-109605896-G-A
• rs2391777
• ENST00000837748.1:n.705C>T

Variant summary

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

The ENST00000837748.1(ENSG00000309005):​n.705C>T variant causes a non coding transcript exon 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: ENSG00000309005 ENST00000837748.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676
• Publications: 5 publications found

Genes affected

ENSG00000309005 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124903210	XR_007063870.1	n.940+313C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309005	ENST00000837748.1	n.705C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000285534	ENST00000650264.1	n.759-34738C>T		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.548 AC: 22737 AN: 41510

American (AMR) AF: 0.463 AC: 7077 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1299 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2864 AN: 5176

South Asian (SAS) AF: 0.581 AC: 2801 AN: 4822

European-Finnish (FIN) AF: 0.345 AC: 3646 AN: 10568

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.385 AC: 26200 AN: 67996

Other (OTH) AF: 0.434 AC: 917 AN: 2112

Alfa AF: 0.427 Hom.: 2478

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2391777; hg19: chr13-110258243;