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: 16 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373422	XR_922784.4	n.150-795C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287305	ENST00000654664.2	n.178-795C>T		intron_variant	Intron 1 of 2
ENSG00000287305	ENST00000826142.1	n.66-795C>T		intron_variant	Intron 1 of 2
ENSG00000287305	ENST00000826143.1	n.34-5757C>T		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs1109037; hg19: chr2-10085722;