rs7089063

chr10-45450941-C-A

Variant summary

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

The NR_120674.1(LOC102724323):n.179+1903G>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 0.258 in 151,484 control chromosomes in the GnomAD database, including 5,287 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 0.26 (5287 hom., cov: 32)
• Consequence: LOC102724323 NR_120674.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724323	NR_120674.1	n.179+1903G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435635.1	n.179+1903G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39116 AN: 151384 Hom.: 5283 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.258 AC: 39132 AN: 151484 Hom.: 5287 Cov.: 32 AF XY: 0.260 AC XY: 19268 AN XY: 74016

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.241

Alfa AF: 0.247 Hom.: 1010

Bravo AF: 0.251

Asia WGS AF: 0.204 AC: 706 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.32
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7089063; hg19: chr10-45946389;