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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837748.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309005	ENST00000837748.1		n.35T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000285534	ENST00000650264.1		n.759-35563T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1411765;

hg19: chr13-110259068;