ENST00000658199.1:n.491+3496A>G

Variant names:

• chr11-114360533-T-C
• rs11214966
• ENST00000658199.1:n.491+3496A>G

Variant summary

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

The ENST00000658199.1(ENSG00000256195):​n.491+3496A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,150 control chromosomes in the GnomAD database, including 1,632 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 (1632 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000256195 ENST00000658199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 15 publications found

Genes affected

ENSG00000256195 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928940	NR_120567.1	n.*102A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256195	ENST00000658199.1	n.491+3496A>G		intron_variant	Intron 3 of 3
ENSG00000256195	ENST00000534904.2	n.*102A>G		downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19628 AN: 152032 Hom.: 1626 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.117

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.129 AC: 19666 AN: 152150 Hom.: 1632 Cov.: 32 AF XY: 0.129 AC XY: 9597 AN XY: 74384

African (AFR) AF: 0.226 AC: 9360 AN: 41488

American (AMR) AF: 0.140 AC: 2139 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 302 AN: 3470

East Asian (EAS) AF: 0.125 AC: 649 AN: 5184

South Asian (SAS) AF: 0.0742 AC: 358 AN: 4828

European-Finnish (FIN) AF: 0.107 AC: 1137 AN: 10586

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0798 AC: 5424 AN: 67988

Other (OTH) AF: 0.118 AC: 250 AN: 2112

Alfa AF: 0.0939 Hom.: 2367

Bravo AF: 0.136

Asia WGS AF: 0.115 AC: 402 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.80
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11214966; hg19: chr11-114231255;