chr4-19781529-C-T

Variant names:

• chr4-19781529-C-T
• rs11936151
• ENST00000511431.1:n.289-74747C>T

Variant summary

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

The ENST00000511431.1(ENSG00000248515):​n.289-74747C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,122 control chromosomes in the GnomAD database, including 1,529 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 (1529 hom., cov: 32)
• Consequence: ENSG00000248515 ENST00000511431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 1 publications found

Genes affected

ENSG00000248515 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374511	NR_188378.1	n.236-74750C>T		intron_variant	Intron 1 of 3
LOC105374511	NR_188379.1	n.307-74747C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248515	ENST00000511431.1	n.289-74747C>T		intron_variant	Intron 2 of 3	3
ENSG00000248515	ENST00000655810.1	n.33-74747C>T		intron_variant	Intron 1 of 3
ENSG00000248515	ENST00000661892.1	n.227-52396C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19833 AN: 152004 Hom.: 1528 Cov.: 32

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0749

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.130 AC: 19824 AN: 152122 Hom.: 1529 Cov.: 32 AF XY: 0.128 AC XY: 9537 AN XY: 74358

African (AFR) AF: 0.0660 AC: 2739 AN: 41514

American (AMR) AF: 0.125 AC: 1911 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3472

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5172

South Asian (SAS) AF: 0.0750 AC: 362 AN: 4828

European-Finnish (FIN) AF: 0.173 AC: 1824 AN: 10568

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11484 AN: 67980

Other (OTH) AF: 0.134 AC: 283 AN: 2110

Alfa AF: 0.148 Hom.: 1138

Bravo AF: 0.124

Asia WGS AF: 0.0440 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.54
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs11936151; hg19: chr4-19783152;