11-49537620-T-C

Variant names:

• chr11-49537620-T-C
• rs1814175
• ENST00000805121.1:n.390+16742A>G

Variant summary

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

The ENST00000805121.1(ENSG00000304646):​n.390+16742A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,456 control chromosomes in the GnomAD database, including 20,426 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 0.50 (20426 hom., cov: 31)
• Consequence: ENSG00000304646 ENST00000805121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 33 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805121.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304646	ENST00000805121.1		n.390+16742A>G		intron	N/A
	ENSG00000304646	ENST00000805122.1		n.404-2176A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75176 AN: 151338 Hom.: 20412 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.497 AC: 75210 AN: 151456 Hom.: 20426 Cov.: 31 AF XY: 0.498 AC XY: 36796 AN XY: 73952

African (AFR) AF: 0.261 AC: 10810 AN: 41360

American (AMR) AF: 0.612 AC: 9297 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2289 AN: 3462

East Asian (EAS) AF: 0.537 AC: 2744 AN: 5112

South Asian (SAS) AF: 0.512 AC: 2453 AN: 4794

European-Finnish (FIN) AF: 0.574 AC: 6023 AN: 10502

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39568 AN: 67732

Other (OTH) AF: 0.554 AC: 1166 AN: 2106

Alfa AF: 0.541 Hom.: 37154

Bravo AF: 0.493

Asia WGS AF: 0.475 AC: 1652 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.38
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1814175; hg19: chr11-49559172;