rs11668269

Positions:

• chr19-22331158-G-A
• chr19-22331158-G-C
• chr19-22331158-G-T

Variant summary

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

The XR_001754094.2(LOC105372330):​n.211+212C>T 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 0.573 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

Genes affected

LOC105372330 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105372330	XR_001754094.2	n.211+212C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.587

Alfa AF: 0.560 Hom.: 31448

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11668269; hg19: chr19-22513960;