rs1011229

Positions:

• chr2-52825542-T-C

Variant summary

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

The ENST00000421575.6(ENSG00000228033):​n.207+71701A>G 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 0.0368 in 151,896 control chromosomes in the GnomAD database, including 337 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 0.037 (337 hom., cov: 32)
• Consequence: ENST00000421575.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369165	XR_002959384.2	n.171+71701A>G		intron_variant, non_coding_transcript_variant
LOC105369165	XR_001739464.3	n.328+71701A>G		intron_variant, non_coding_transcript_variant
LOC105369165	XR_002959385.2	n.329-30686A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000421575.6	n.207+71701A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000443237.1	n.119+71701A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000668945.1	n.219+71701A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0367 AC: 5574 AN: 151778 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0168

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0850

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00481

Gnomad OTH AF: 0.0508

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

GnomAD4 genome AF: 0.0368 AC: 5583 AN: 151896 Hom.: 337 Cov.: 32 AF XY: 0.0420 AC XY: 3117 AN XY: 74264

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0168

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.0850

Gnomad4 NFE AF: 0.00481

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0216 Hom.: 14

Bravo AF: 0.0420

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1011229; hg19: chr2-53052680;