11-49538486-A-T

Variant names:

• chr11-49538486-A-T
• rs3913231
• ENST00000805121.1:n.390+15876T>A

Variant summary

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

The ENST00000805121.1(ENSG00000304646):​n.390+15876T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0724 in 151,954 control chromosomes in the GnomAD database, including 554 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 0.072 (554 hom., cov: 32)
• Consequence: ENSG00000304646 ENST00000805121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839
• Publications: 3 publications found

Genes affected

ENSG00000304646 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 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
ENSG00000304646	ENST00000805121.1	n.390+15876T>A		intron_variant	Intron 3 of 3
ENSG00000304646	ENST00000805122.1	n.404-3042T>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0724 AC: 10988 AN: 151836 Hom.: 551 Cov.: 32

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0946

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.0471

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0788

Gnomad OTH AF: 0.0756

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

GnomAD4 genome AF: 0.0724 AC: 10996 AN: 151954 Hom.: 554 Cov.: 32 AF XY: 0.0747 AC XY: 5552 AN XY: 74276

African (AFR) AF: 0.0308 AC: 1280 AN: 41542

American (AMR) AF: 0.0952 AC: 1450 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3470

East Asian (EAS) AF: 0.165 AC: 849 AN: 5132

South Asian (SAS) AF: 0.226 AC: 1090 AN: 4822

European-Finnish (FIN) AF: 0.0471 AC: 500 AN: 10610

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0788 AC: 5346 AN: 67834

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0689 Hom.: 56

Bravo AF: 0.0702

Asia WGS AF: 0.241 AC: 837 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.7
DANN	Benign	0.67
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs3913231; hg19: chr11-49560038;