1-11911692-G-A

Variant names:

• chr1-11911692-G-A
• rs11800086
• ENST00000649268.2:n.322+103G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

ENSG00000285646 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649268.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285646	ENST00000649268.2		n.322+103G>A		intron	N/A
	ENSG00000285646	ENST00000650448.1		n.240-1126G>A		intron	N/A
	ENSG00000285646	ENST00000658167.2		n.236-1010G>A		intron	N/A

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

African (AFR) AF: 0.545 AC: 22604 AN: 41450

American (AMR) AF: 0.364 AC: 5547 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3472

East Asian (EAS) AF: 0.464 AC: 2405 AN: 5178

South Asian (SAS) AF: 0.429 AC: 2070 AN: 4820

European-Finnish (FIN) AF: 0.489 AC: 5153 AN: 10544

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22902 AN: 67960

Other (OTH) AF: 0.392 AC: 823 AN: 2100

Alfa AF: 0.343 Hom.: 11917

Bravo AF: 0.405

Asia WGS AF: 0.459 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.57
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs11800086; hg19: chr1-11971749;