rs13026414

Positions:

• chr2-57706920-C-T

Variant summary

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

The XR_245007.4(LOC101927235):​n.731+337C>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 0.29 in 152,104 control chromosomes in the GnomAD database, including 7,766 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 0.29 (7766 hom., cov: 32)
• Consequence: LOC101927235 XR_245007.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

Genes affected

LOC101927235 (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 (NFE) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927235	XR_245007.4	n.731+337C>T		intron_variant, non_coding_transcript_variant
LOC101927235	XR_940113.3	n.554+337C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44146 AN: 151986 Hom.: 7769 Cov.: 32

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.290 AC: 44136 AN: 152104 Hom.: 7766 Cov.: 32 AF XY: 0.282 AC XY: 20962 AN XY: 74360

Gnomad4 AFR AF: 0.0967

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.337

Alfa AF: 0.352 Hom.: 4941

Bravo AF: 0.289

Asia WGS AF: 0.226 AC: 786 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	0.99
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13026414; hg19: chr2-57934055;