19-22331158-G-A

Variant names:

• chr19-22331158-G-A
• rs11668269
• XR_001754094.2:n.211+212C>T

Variant summary

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

The XR_001754094.2(LOC105372330):​n.211+212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,774 control chromosomes in the GnomAD database, including 25,142 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 0.57 (25142 hom., cov: 33)
• Consequence: LOC105372330 XR_001754094.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 8 publications found

Genes affected

LOC105372330 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86918 AN: 151656 Hom.: 25101 Cov.: 33

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.573 AC: 87015 AN: 151774 Hom.: 25142 Cov.: 33 AF XY: 0.580 AC XY: 43035 AN XY: 74212

African (AFR) AF: 0.577 AC: 23875 AN: 41380

American (AMR) AF: 0.579 AC: 8833 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2361 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3624 AN: 5122

South Asian (SAS) AF: 0.760 AC: 3667 AN: 4824

European-Finnish (FIN) AF: 0.555 AC: 5852 AN: 10552

Middle Eastern (MID) AF: 0.677 AC: 195 AN: 288

European-Non Finnish (NFE) AF: 0.545 AC: 36964 AN: 67864

Other (OTH) AF: 0.587 AC: 1239 AN: 2110

Alfa AF: 0.560 Hom.: 40026

Bravo AF: 0.567

Asia WGS AF: 0.751 AC: 2612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.34
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs11668269; hg19: chr19-22513960;