rs10494321

chr1-157938654-A-G

Variant summary

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

The NR_135760.1(LOC105371458):n.340-7002A>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 0.313 in 152,096 control chromosomes in the GnomAD database, including 7,926 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 0.31 (7926 hom., cov: 32)
• Consequence: LOC105371458 NR_135760.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371458	NR_135760.1	n.340-7002A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000452528.5	n.333-7002A>G		intron_variant, non_coding_transcript_variant		2
	ENST00000422062.1	n.262-4010A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47498 AN: 151978 Hom.: 7912 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.313 AC: 47554 AN: 152096 Hom.: 7926 Cov.: 32 AF XY: 0.310 AC XY: 23021 AN XY: 74352

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0787

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.272

Alfa AF: 0.310 Hom.: 15497

Bravo AF: 0.297

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.5
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494321; hg19: chr1-157908444;