rs1109037

chr2-9945593-G-Achr2-9945593-G-C

Variant summary

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

The ENST00000654664.1(ENSG00000287305):n.114-795C>T 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 0.475 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: ENST00000654664.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105373422	XR_922784.4	n.150-795C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654664.1	n.114-795C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.477

Alfa AF: 0.502 Hom.: 20011

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1109037; hg19: chr2-10085722;