chr10-67849782-C-A

Variant names:

• chr10-67849782-C-A
• rs7097008
• ENST00000610279.1:n.258C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

ENSG00000272892 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000610279.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272892	ENST00000610279.1	TSL:6	n.258C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000272892	ENST00000743596.1		n.89C>A		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.692 AC: 18 AN: 26

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.531 AC: 21990 AN: 41394

American (AMR) AF: 0.561 AC: 8553 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2419 AN: 3470

East Asian (EAS) AF: 0.151 AC: 781 AN: 5160

South Asian (SAS) AF: 0.454 AC: 2181 AN: 4802

European-Finnish (FIN) AF: 0.591 AC: 6233 AN: 10540

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46111 AN: 67932

Other (OTH) AF: 0.608 AC: 1284 AN: 2112

Alfa AF: 0.647 Hom.: 47382

Bravo AF: 0.585

Asia WGS AF: 0.378 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7097008; hg19: chr10-69609540;