2-22501721-C-T

Position:

• chr2-22501721-C-T

Variant summary

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

The ENST00000450551.1(ENSG00000228999):​n.70+29315G>A 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 0.0387 in 152,118 control chromosomes in the GnomAD database, including 234 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 0.039 (234 hom., cov: 32)
• Consequence: ENST00000450551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0997 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01830	XR_002959374.1	n.249+29315G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000450551.1	n.70+29315G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0387 AC: 5883 AN: 152000 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0210

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.000584

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.00725

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0387 AC: 5893 AN: 152118 Hom.: 234 Cov.: 32 AF XY: 0.0389 AC XY: 2892 AN XY: 74370

Gnomad4 AFR AF: 0.0869

Gnomad4 AMR AF: 0.0209

Gnomad4 ASJ AF: 0.00922

Gnomad4 EAS AF: 0.000585

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.00725

Gnomad4 NFE AF: 0.0185

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0225 Hom.: 18

Bravo AF: 0.0395

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17043944; hg19: chr2-22724593;