rs2261151

Positions:

• chr14-48773011-C-T

Variant summary

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

The XR_007064152.1(LOC105378178):​n.346-36543G>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 0.204 in 152,058 control chromosomes in the GnomAD database, including 3,786 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 0.20 (3786 hom., cov: 32)
• Consequence: LOC105378178 XR_007064152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

Genes affected

LOC105378178 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378178	XR_007064152.1	n.346-36543G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30914 AN: 151940 Hom.: 3781 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.204 AC: 30957 AN: 152058 Hom.: 3786 Cov.: 32 AF XY: 0.206 AC XY: 15279 AN XY: 74332

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.211

Alfa AF: 0.165 Hom.: 1211

Bravo AF: 0.223

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2261151; hg19: chr14-49242214;