chr11-47919373-T-C

Variant names:

• chr11-47919373-T-C
• rs747782
• ENST00000848482.1:n.515+11485A>G

Variant summary

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

The ENST00000848482.1(ENSG00000310235):​n.515+11485A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,012 control chromosomes in the GnomAD database, including 5,695 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 0.26 (5695 hom., cov: 32)
• Consequence: ENSG00000310235 ENST00000848482.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82
• Publications: 30 publications found

Genes affected

ENSG00000310235 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 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
ENSG00000310235	ENST00000848482.1	n.515+11485A>G		intron_variant	Intron 1 of 1
ENSG00000310235	ENST00000848483.1	n.512+11485A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38773 AN: 151894 Hom.: 5696 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.255 AC: 38802 AN: 152012 Hom.: 5695 Cov.: 32 AF XY: 0.255 AC XY: 18981 AN XY: 74320

African (AFR) AF: 0.404 AC: 16730 AN: 41444

American (AMR) AF: 0.184 AC: 2807 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1367 AN: 5142

South Asian (SAS) AF: 0.189 AC: 912 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2451 AN: 10582

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13211 AN: 67994

Other (OTH) AF: 0.215 AC: 454 AN: 2110

Alfa AF: 0.206 Hom.: 13653

Bravo AF: 0.258

Asia WGS AF: 0.188 AC: 655 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.60
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs747782; hg19: chr11-47940925;