rs11893063

Positions:

• chr2-198737201-G-A

Variant summary

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

The ENST00000440609.1(ENSG00000225421):​n.98+35058C>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 0.37 in 150,896 control chromosomes in the GnomAD database, including 12,038 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 0.37 (12038 hom., cov: 29)
• Consequence: ENST00000440609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373831	XR_923759.3	n.72+35058C>T		intron_variant, non_coding_transcript_variant
LOC105373831	XR_923760.2	n.72+35058C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000440609.1	n.98+35058C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.370 AC: 55763 AN: 150798 Hom.: 12043 Cov.: 29

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.370 AC: 55771 AN: 150896 Hom.: 12038 Cov.: 29 AF XY: 0.376 AC XY: 27685 AN XY: 73610

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.379

Alfa AF: 0.438 Hom.: 14717

Bravo AF: 0.343

Asia WGS AF: 0.324 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.6
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: rs11893063; hg19: chr2-199601925;