rs2849165

Variant names:

• chr11-116817762-C-T
• rs2849165
• ENST00000814126.1:n.135+3422C>T

Variant summary

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

The ENST00000814126.1(ENSG00000305923):​n.135+3422C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 151,970 control chromosomes in the GnomAD database, including 1,818 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 0.13 (1818 hom., cov: 31)
• Consequence: ENSG00000305923 ENST00000814126.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 4 publications found

Genes affected

ENSG00000305923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 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
ENSG00000305923	ENST00000814126.1	n.135+3422C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20390 AN: 151852 Hom.: 1820 Cov.: 31

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.134 AC: 20400 AN: 151970 Hom.: 1818 Cov.: 31 AF XY: 0.131 AC XY: 9706 AN XY: 74292

African (AFR) AF: 0.0388 AC: 1608 AN: 41412

American (AMR) AF: 0.121 AC: 1848 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3470

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5166

South Asian (SAS) AF: 0.119 AC: 573 AN: 4822

European-Finnish (FIN) AF: 0.136 AC: 1434 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13591 AN: 67948

Other (OTH) AF: 0.146 AC: 307 AN: 2108

Alfa AF: 0.161 Hom.: 268

Bravo AF: 0.127

Asia WGS AF: 0.0550 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.65
DANN	Benign	0.25
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2849165; hg19: chr11-116688478;