rs2209852

Variant names:

• chr13-94865368-A-G
• rs2209852
• NR_110754.1:n.257-40096A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110754.1(LOC101927284):​n.257-40096A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,954 control chromosomes in the GnomAD database, including 20,217 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 0.51 (20217 hom., cov: 32)
• Consequence: LOC101927284 NR_110754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 3 publications found

Genes affected

LOC101927284 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927284	NR_110754.1	n.257-40096A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76857 AN: 151832 Hom.: 20190 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.506 AC: 76925 AN: 151954 Hom.: 20217 Cov.: 32 AF XY: 0.495 AC XY: 36721 AN XY: 74254

African (AFR) AF: 0.631 AC: 26158 AN: 41430

American (AMR) AF: 0.485 AC: 7395 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1512 AN: 3462

East Asian (EAS) AF: 0.175 AC: 906 AN: 5166

South Asian (SAS) AF: 0.293 AC: 1415 AN: 4824

European-Finnish (FIN) AF: 0.423 AC: 4451 AN: 10532

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33471 AN: 67966

Other (OTH) AF: 0.483 AC: 1019 AN: 2108

Alfa AF: 0.491 Hom.: 28905

Bravo AF: 0.520

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.0
DANN	Benign	0.51
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs2209852; hg19: chr13-95517622;