rs11084033

Variant names:

• chr19-50850699-C-A
• rs11084033
• ENST00000598079.1:n.214-212C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-50850699-C-A
• chr19-50850699-C-T

Variant summary

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

The ENST00000598079.1(ENSG00000267968):​n.214-212C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,998 control chromosomes in the GnomAD database, including 3,558 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 0.20 (3558 hom., cov: 31)
• Consequence: ENSG00000267968 ENST00000598079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 6 publications found

Genes affected

ENSG00000267968 (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 (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372441	NR_131203.1	n.214-212C>A		intron_variant	Intron 2 of 2
LOC105372441	NR_131205.1	n.231-212C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267968	ENST00000598079.1	n.214-212C>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29881 AN: 151880 Hom.: 3554 Cov.: 31

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.197 AC: 29894 AN: 151998 Hom.: 3558 Cov.: 31 AF XY: 0.200 AC XY: 14834 AN XY: 74288

African (AFR) AF: 0.0845 AC: 3507 AN: 41480

American (AMR) AF: 0.301 AC: 4602 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3466

East Asian (EAS) AF: 0.350 AC: 1803 AN: 5158

South Asian (SAS) AF: 0.142 AC: 683 AN: 4814

European-Finnish (FIN) AF: 0.313 AC: 3299 AN: 10550

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.215 AC: 14622 AN: 67942

Other (OTH) AF: 0.198 AC: 416 AN: 2106

Alfa AF: 0.202 Hom.: 1845

Bravo AF: 0.192

Asia WGS AF: 0.257 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.86
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs11084033; hg19: chr19-51353955;