rs1956932

chr14-24498614-A-G

Variant summary

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

The NR_110032.1(LOC101927045):n.1479-2946A>G 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 0.087 in 152,182 control chromosomes in the GnomAD database, including 657 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 0.087 (657 hom., cov: 32)
• Consequence: LOC101927045 NR_110032.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927045	NR_110032.1	n.1479-2946A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656888.1	n.281-2946A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13244 AN: 152064 Hom.: 656 Cov.: 32

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0113

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.0870 AC: 13246 AN: 152182 Hom.: 657 Cov.: 32 AF XY: 0.0857 AC XY: 6377 AN XY: 74406

Gnomad4 AFR AF: 0.0518

Gnomad4 AMR AF: 0.0720

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0840

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.108 Hom.: 1240

Bravo AF: 0.0821

Asia WGS AF: 0.0470 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.78
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1956932; hg19: chr14-24967820;