rs2243737

Positions:

• chr20-52893967-T-A
• chr20-52893967-T-C

Variant summary

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

The XR_936864.3(LOC105372668):​n.287+1173A>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 0.368 in 151,940 control chromosomes in the GnomAD database, including 10,536 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 (10536 hom., cov: 32)
• Consequence: LOC105372668 XR_936864.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418

Genes affected

LOC105372668 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372668	XR_936864.3	n.287+1173A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55933 AN: 151822 Hom.: 10532 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.368 AC: 55954 AN: 151940 Hom.: 10536 Cov.: 32 AF XY: 0.379 AC XY: 28113 AN XY: 74238

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.368

Alfa AF: 0.355 Hom.: 1186

Bravo AF: 0.362

Asia WGS AF: 0.506 AC: 1754 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243737; hg19: chr20-51510506;