rs1411765

Variant names:

• chr13-109606721-A-G
• rs1411765
• ENST00000837748.1:n.35T>C

Variant summary

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

The ENST00000837748.1(ENSG00000309005):​n.35T>C 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 0.508 in 152,110 control chromosomes in the GnomAD database, including 20,431 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 0.51 (20431 hom., cov: 33)
• Consequence: ENSG00000309005 ENST00000837748.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903210	XR_007063870.1	n.428T>C		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309005	ENST00000837748.1	n.35T>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000285534	ENST00000650264.1	n.759-35563T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77222 AN: 151992 Hom.: 20395 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.508 AC: 77310 AN: 152110 Hom.: 20431 Cov.: 33 AF XY: 0.513 AC XY: 38122 AN XY: 74354

African (AFR) AF: 0.639 AC: 26495 AN: 41492

American (AMR) AF: 0.541 AC: 8273 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3470

East Asian (EAS) AF: 0.608 AC: 3145 AN: 5170

South Asian (SAS) AF: 0.613 AC: 2958 AN: 4826

European-Finnish (FIN) AF: 0.402 AC: 4248 AN: 10560

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.430 AC: 29253 AN: 67976

Other (OTH) AF: 0.497 AC: 1050 AN: 2114

Alfa AF: 0.462 Hom.: 10683

Bravo AF: 0.520

Asia WGS AF: 0.566 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.52
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1411765; hg19: chr13-110259068;