rs11084033

chr19-50850699-C-Achr19-50850699-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_131205.1(LOC105372441):n.231-212C>A variant causes a intron, non coding transcript 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: LOC105372441 NR_131205.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105372441	NR_131205.1	n.231-212C>A		intron_variant, non_coding_transcript_variant
LOC105372441	NR_131203.1	n.214-212C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000598079.1	n.214-212C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0845

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.198

Alfa AF: 0.197 Hom.: 1085

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11084033; hg19: chr19-51353955;