rs7097008

Variant names:

• chr10-67849782-C-A
• rs7097008
• ENST00000610279.1:n.258C>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: ENSG00000272892 ENST00000610279.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

ENSG00000272892 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272892	ENST00000610279.1	n.258C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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;