rs7097008

Positions:

• chr10-67849782-C-A

Variant summary

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

The ENST00000610279.1(ENSG00000272892):​n.258C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,890 control chromosomes in the GnomAD database, including 27,777 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 0.59 (27770 hom., cov: 31)
  • Exomes 𝑓: 0.63 (7 hom.)
• Consequence: ENST00000610279.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000610279.1	n.258C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90173 AN: 151740 Hom.: 27760 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.605

GnomAD4 exome AF: 0.625 AC: 20 AN: 32 Hom.: 7 Cov.: 0 AF XY: 0.682 AC XY: 15 AN XY: 22

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.692

GnomAD4 genome AF: 0.594 AC: 90216 AN: 151858 Hom.: 27770 Cov.: 31 AF XY: 0.586 AC XY: 43498 AN XY: 74246

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.608

Alfa AF: 0.661 Hom.: 33263

Bravo AF: 0.585

Asia WGS AF: 0.378 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7097008; hg19: chr10-69609540;