rs10493293

chr1-60673496-G-A

Variant summary

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

The NR_110628.1(LOC101926964):n.464-10471C>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 0.059 in 152,144 control chromosomes in the GnomAD database, including 542 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 0.059 (542 hom., cov: 33)
• Consequence: LOC101926964 NR_110628.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429

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 (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101926964	NR_110628.1	n.464-10471C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667362.1	n.522-10471C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8942 AN: 152026 Hom.: 538 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0437

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.0719

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00957

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0590 AC: 8976 AN: 152144 Hom.: 542 Cov.: 33 AF XY: 0.0594 AC XY: 4422 AN XY: 74392

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0438

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.0718

Gnomad4 SAS AF: 0.0586

Gnomad4 FIN AF: 0.0385

Gnomad4 NFE AF: 0.00957

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0235 Hom.: 153

Bravo AF: 0.0633

Asia WGS AF: 0.0790 AC: 275 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	3.0
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493293; hg19: chr1-61139168;