chr22-26869559-G-A

Position:

• chr22-26869559-G-A

Variant summary

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

The NR_146604.1(LOC110091768):​n.794+7454G>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 0.0358 in 152,308 control chromosomes in the GnomAD database, including 161 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 0.036 (161 hom., cov: 32)
• Consequence: LOC110091768 NR_146604.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

Genes affected

LINC01422 (HGNC:50728): (long intergenic non-protein coding RNA 1422)

LOC110091768 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC110091768	NR_146604.1	n.794+7454G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01422	ENST00000670559.1	n.335+7454G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0358 AC: 5448 AN: 152192 Hom.: 160 Cov.: 32

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.00395

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0358 AC: 5455 AN: 152308 Hom.: 161 Cov.: 32 AF XY: 0.0343 AC XY: 2556 AN XY: 74496

Gnomad4 AFR AF: 0.0798

Gnomad4 AMR AF: 0.0298

Gnomad4 ASJ AF: 0.00923

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0154

Gnomad4 FIN AF: 0.00395

Gnomad4 NFE AF: 0.0203

Gnomad4 OTH AF: 0.0351

Alfa AF: 0.0335 Hom.: 25

Bravo AF: 0.0396

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2331311; hg19: chr22-27265522;