22-19304923-T-G

Position:

• chr22-19304923-T-G

Variant summary

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

The ENST00000664918.1(ENSG00000287146):​n.362+12593T>G 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 0.291 in 152,006 control chromosomes in the GnomAD database, including 7,121 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 0.29 (7121 hom., cov: 31)
• Consequence: ENST00000664918.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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 (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372859	XR_938002.3	n.384+12593T>G		intron_variant, non_coding_transcript_variant
LOC105372859	XR_938000.3	n.384+12593T>G		intron_variant, non_coding_transcript_variant
LOC105372859	XR_938001.3	n.384+12593T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664918.1	n.362+12593T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44140 AN: 151888 Hom.: 7113 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.291 AC: 44172 AN: 152006 Hom.: 7121 Cov.: 31 AF XY: 0.287 AC XY: 21311 AN XY: 74294

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.261

Alfa AF: 0.259 Hom.: 1377

Bravo AF: 0.303

Asia WGS AF: 0.232 AC: 806 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	3.0
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8135222; hg19: chr22-19292446;