1-22153666-A-G

Variant summary

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

The ENST00000648968.1(ENSG00000285873):n.56-1237A>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 0.426 in 151,840 control chromosomes in the GnomAD database, including 13,982 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 0.43 (13982 hom., cov: 31)
• Consequence: ENST00000648968.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

Genes affected

(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 (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376845	XR_947050.1	n.54-1237A>G		intron_variant, non_coding_transcript_variant
LOC105376845	XR_947051.3	n.143-1237A>G		intron_variant, non_coding_transcript_variant
LOC105376845	XR_947052.1	n.270-1237A>G		intron_variant, non_coding_transcript_variant
LOC105376845	XR_947056.2	n.143-1237A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648968.1	n.56-1237A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64581 AN: 151722 Hom.: 13966 Cov.: 31

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.426 AC: 64644 AN: 151840 Hom.: 13982 Cov.: 31 AF XY: 0.422 AC XY: 31330 AN XY: 74228

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.423

Alfa AF: 0.415 Hom.: 9082

Bravo AF: 0.433

Asia WGS AF: 0.415 AC: 1439 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	2.6
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7517829; hg19: chr1-22480159;