1-11911692-G-A

Position:

• chr1-11911692-G-A

Variant summary

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

The ENST00000649268.2(ENSG00000285646):​n.322+103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,972 control chromosomes in the GnomAD database, including 13,773 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 0.41 (13773 hom., cov: 32)
• Consequence: ENSG00000285646 ENST00000649268.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782

Genes affected

ENSG00000285646 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903843	XR_007065464.1	n.97+103G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285646	ENST00000649268.2	n.322+103G>A		intron_variant
ENSG00000285646	ENST00000650448.1	n.240-1126G>A		intron_variant
ENSG00000285646	ENST00000658167.1	n.235-1010G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62444 AN: 151852 Hom.: 13746 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.411 AC: 62526 AN: 151972 Hom.: 13773 Cov.: 32 AF XY: 0.416 AC XY: 30922 AN XY: 74272

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.392

Alfa AF: 0.329 Hom.: 8328

Bravo AF: 0.405

Asia WGS AF: 0.459 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11800086; hg19: chr1-11971749;