rs918629

Positions:

• chr5-95965759-G-A

Variant summary

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

The NR_130776.1(LOC101929710):​n.36+3723G>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 0.393 in 152,050 control chromosomes in the GnomAD database, including 13,970 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 0.39 (13970 hom., cov: 32)
• Consequence: LOC101929710 NR_130776.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929710	NR_130776.1	n.36+3723G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000502645.2	n.36+3723G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000506070.1	n.319-508C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000511775.1	n.35+3723G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59602 AN: 151932 Hom.: 13932 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.393 AC: 59688 AN: 152050 Hom.: 13970 Cov.: 32 AF XY: 0.400 AC XY: 29736 AN XY: 74332

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.351

Alfa AF: 0.270 Hom.: 12460

Bravo AF: 0.407

Asia WGS AF: 0.642 AC: 2228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs918629; hg19: chr5-95301463;