chr10-87658973-C-A

Variant names:

• chr10-87658973-C-A
• rs2180968
• ENST00000438082.1:n.189C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000438082.1(ENSG00000225913):​n.189C>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 0.337 in 152,224 control chromosomes in the GnomAD database, including 9,069 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 0.34 (9061 hom., cov: 33)
  • Exomes 𝑓: 0.33 (8 hom.)
• Consequence: ENSG00000225913 ENST00000438082.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641
• Publications: 8 publications found

Genes affected

ENSG00000225913 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438082.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225913	ENST00000438082.1	TSL:3	n.189C>A		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000225913	ENST00000804457.1		n.451C>A		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000225913	ENST00000804458.1		n.310C>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51191 AN: 151958 Hom.: 9057 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0782

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.338

GnomAD4 exome AF: 0.331 AC: 49 AN: 148 Hom.: 8 Cov.: 0 AF XY: 0.340 AC XY: 36 AN XY: 106

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 4 AN: 8

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.339 AC: 38 AN: 112

Other (OTH) AF: 0.250 AC: 5 AN: 20

GnomAD4 genome AF: 0.337 AC: 51224 AN: 152076 Hom.: 9061 Cov.: 33 AF XY: 0.327 AC XY: 24327 AN XY: 74356

African (AFR) AF: 0.281 AC: 11649 AN: 41470

American (AMR) AF: 0.316 AC: 4839 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1050 AN: 3466

East Asian (EAS) AF: 0.0784 AC: 406 AN: 5178

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4820

European-Finnish (FIN) AF: 0.306 AC: 3234 AN: 10572

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.409 AC: 27791 AN: 67966

Other (OTH) AF: 0.336 AC: 708 AN: 2108

Alfa AF: 0.259 Hom.: 930

Bravo AF: 0.336

Asia WGS AF: 0.182 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.53
DANN	Benign	0.71
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2180968; hg19: chr10-89418730;