rs1250220

Positions:

• chr2-215455327-C-A
• chr2-215455327-C-G
• chr2-215455327-C-T

Variant summary

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

The NR_110607.1(LOC102724849):​n.20-1565C>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 0.52 in 151,898 control chromosomes in the GnomAD database, including 21,288 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 0.52 (21288 hom., cov: 32)
• Consequence: LOC102724849 NR_110607.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724849	NR_110607.1	n.20-1565C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654128.1	n.111+1494C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78913 AN: 151780 Hom.: 21284 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.520 AC: 78948 AN: 151898 Hom.: 21288 Cov.: 32 AF XY: 0.526 AC XY: 39007 AN XY: 74228

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.541

Alfa AF: 0.526 Hom.: 21951

Bravo AF: 0.528

Asia WGS AF: 0.630 AC: 2191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1250220; hg19: chr2-216320050;