rs1109037

Variant names:

• chr2-9945593-G-A
• rs1109037
• ENST00000654664.2:n.178-795C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-9945593-G-A
• chr2-9945593-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654664.2(ENSG00000287305):​n.178-795C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,940 control chromosomes in the GnomAD database, including 17,418 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 0.48 (17418 hom., cov: 31)
• Consequence: ENSG00000287305 ENST00000654664.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 17 publications found

Genes affected

ENSG00000287305 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654664.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287305	ENST00000654664.2		n.178-795C>T		intron	N/A
	ENSG00000287305	ENST00000826142.1		n.66-795C>T		intron	N/A
	ENSG00000287305	ENST00000826143.1		n.34-5757C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72147 AN: 151822 Hom.: 17407 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.475 AC: 72183 AN: 151940 Hom.: 17418 Cov.: 31 AF XY: 0.470 AC XY: 34879 AN XY: 74256

African (AFR) AF: 0.430 AC: 17818 AN: 41444

American (AMR) AF: 0.490 AC: 7474 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1686 AN: 3464

East Asian (EAS) AF: 0.440 AC: 2270 AN: 5160

South Asian (SAS) AF: 0.406 AC: 1955 AN: 4814

European-Finnish (FIN) AF: 0.428 AC: 4515 AN: 10544

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34868 AN: 67934

Other (OTH) AF: 0.477 AC: 1006 AN: 2108

Alfa AF: 0.497 Hom.: 53771

Bravo AF: 0.479

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.062
DANN	Benign	0.54
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1109037;

hg19: chr2-10085722;