rs2217448

Positions:

• chr14-82043733-C-T

Variant summary

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

The XR_007064292.1(LOC107984704):​n.842-30195C>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 0.11 in 151,682 control chromosomes in the GnomAD database, including 1,147 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 0.11 (1147 hom., cov: 32)
• Consequence: LOC107984704 XR_007064292.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

Genes affected

LOC107984704 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984704	XR_007064292.1	n.842-30195C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16663 AN: 151564 Hom.: 1147 Cov.: 32

Gnomad AFR AF: 0.0293

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.110 AC: 16651 AN: 151682 Hom.: 1147 Cov.: 32 AF XY: 0.109 AC XY: 8049 AN XY: 74076

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.124

Alfa AF: 0.137 Hom.: 2082

Bravo AF: 0.105

Asia WGS AF: 0.137 AC: 475 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2217448; hg19: chr14-82510077;