rs261967

chr5-96514546-A-C

Variant summary

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

The NR_130776.1(LOC101929710):n.355-116421A>C 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 0.423 in 151,954 control chromosomes in the GnomAD database, including 13,784 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 0.42 (13784 hom., cov: 31)
• Consequence: LOC101929710 NR_130776.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929710	NR_130776.1	n.355-116421A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000502645.2	n.355-116421A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64180 AN: 151836 Hom.: 13767 Cov.: 31

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.423 AC: 64253 AN: 151954 Hom.: 13784 Cov.: 31 AF XY: 0.431 AC XY: 32001 AN XY: 74254

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.402

Alfa AF: 0.423 Hom.: 5422

Bravo AF: 0.414

Asia WGS AF: 0.450 AC: 1561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.5
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs261967; hg19: chr5-95850250;