rs1116470

Variant names:

• chr11-35072944-T-C
• rs1116470
• ENST00000747995.1:n.136+10105T>C

Variant summary

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

The ENST00000747995.1(ENSG00000297460):​n.136+10105T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,080 control chromosomes in the GnomAD database, including 20,365 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 0.50 (20365 hom., cov: 32)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 5 publications found

Genes affected

ENSG00000297460 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297460	ENST00000747995.1	n.136+10105T>C		intron_variant	Intron 2 of 4
ENSG00000297460	ENST00000747996.1	n.85-15494T>C		intron_variant	Intron 1 of 2
ENSG00000297460	ENST00000747997.1	n.84-15494T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76448 AN: 151964 Hom.: 20361 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.503 AC: 76465 AN: 152080 Hom.: 20365 Cov.: 32 AF XY: 0.509 AC XY: 37810 AN XY: 74350

African (AFR) AF: 0.325 AC: 13478 AN: 41470

American (AMR) AF: 0.599 AC: 9160 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2115 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3893 AN: 5172

South Asian (SAS) AF: 0.688 AC: 3323 AN: 4828

European-Finnish (FIN) AF: 0.514 AC: 5427 AN: 10560

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37237 AN: 67980

Other (OTH) AF: 0.539 AC: 1139 AN: 2114

Alfa AF: 0.527 Hom.: 7779

Bravo AF: 0.499

Asia WGS AF: 0.684 AC: 2379 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs1116470; hg19: chr11-35094491;