ENST00000442124.1:n.165-11G>C

Variant names:

• chr11-117103213-G-C
• rs12269901
• ENST00000442124.1:n.165-11G>C

Variant summary

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

The ENST00000442124.1(ENSG00000224077):​n.165-11G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,816 control chromosomes in the GnomAD database, including 15,108 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 0.41 (15107 hom., cov: 31)
  • Exomes 𝑓: 0.35 (1 hom.)
• Consequence: ENSG00000224077 ENST00000442124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 28 publications found

Genes affected

ENSG00000224077 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442124.1. 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
	ENSG00000224077	ENST00000442124.1	TSL:5	n.165-11G>C		intron	N/A
	ENSG00000224077	ENST00000750474.1		n.541-11G>C		intron	N/A
	ENSG00000224077	ENST00000750475.1		n.538-11G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62583 AN: 151672 Hom.: 15070 Cov.: 31

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.359

GnomAD4 exome AF: 0.346 AC: 9 AN: 26 Hom.: 1 Cov.: 0 AF XY: 0.300 AC XY: 6 AN XY: 20

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 6 AN: 18

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.413 AC: 62667 AN: 151790 Hom.: 15107 Cov.: 31 AF XY: 0.414 AC XY: 30673 AN XY: 74152

African (AFR) AF: 0.679 AC: 28115 AN: 41376

American (AMR) AF: 0.337 AC: 5126 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3466

East Asian (EAS) AF: 0.282 AC: 1458 AN: 5164

South Asian (SAS) AF: 0.421 AC: 2029 AN: 4818

European-Finnish (FIN) AF: 0.370 AC: 3882 AN: 10498

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19950 AN: 67938

Other (OTH) AF: 0.358 AC: 751 AN: 2098

Alfa AF: 0.193 Hom.: 398

Bravo AF: 0.423

Asia WGS AF: 0.395 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs12269901; hg19: chr11-116973929;