ENST00000505339.2:n.441+11195G>T

Variant names:

• chr5-33011880-C-A
• rs4867131
• ENST00000505339.2:n.441+11195G>T

Variant summary

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

The ENST00000505339.2(ENSG00000250697):​n.441+11195G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 151,874 control chromosomes in the GnomAD database, including 1,159 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 0.12 (1159 hom., cov: 32)
• Consequence: ENSG00000250697 ENST00000505339.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.94
• Publications: 2 publications found

Genes affected

ENSG00000250697 (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 (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505339.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105374715	NR_188269.1		n.423-320G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250697	ENST00000505339.2	TSL:3	n.441+11195G>T		intron	N/A
	ENSG00000249102	ENST00000511054.1	TSL:3	n.273+2614C>A		intron	N/A
	ENSG00000251281	ENST00000511840.1	TSL:3	n.187-320G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17858 AN: 151756 Hom.: 1155 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0935

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.118 AC: 17881 AN: 151874 Hom.: 1159 Cov.: 32 AF XY: 0.119 AC XY: 8859 AN XY: 74208

African (AFR) AF: 0.100 AC: 4141 AN: 41428

American (AMR) AF: 0.180 AC: 2744 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0935 AC: 324 AN: 3464

East Asian (EAS) AF: 0.213 AC: 1095 AN: 5144

South Asian (SAS) AF: 0.130 AC: 624 AN: 4812

European-Finnish (FIN) AF: 0.134 AC: 1410 AN: 10516

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7200 AN: 67958

Other (OTH) AF: 0.126 AC: 266 AN: 2106

Alfa AF: 0.111 Hom.: 2531

Bravo AF: 0.124

Asia WGS AF: 0.197 AC: 684 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	0.0010
DANN	Benign	0.22
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs4867131; hg19: chr5-33011986;