rs11668269

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr19-22331158-G-A
• chr19-22331158-G-C
• chr19-22331158-G-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372330	XR_001754094.2	n.211+212C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;