rs1951865

chr14-53906123-G-T

Variant summary

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

The XR_001750978.2(LOC107984676):n.308+9144C>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 0.296 in 151,916 control chromosomes in the GnomAD database, including 7,357 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 0.30 (7357 hom., cov: 32)
• Consequence: LOC107984676 XR_001750978.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

Genes affected

LOC107984676 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984676	XR_001750978.2	n.308+9144C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45019 AN: 151800 Hom.: 7359 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.296 AC: 45011 AN: 151916 Hom.: 7357 Cov.: 32 AF XY: 0.291 AC XY: 21582 AN XY: 74232

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.288

Alfa AF: 0.343 Hom.: 4365

Bravo AF: 0.290

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.90
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1951865; hg19: chr14-54372841;