10-3011651-C-T

Variant names:

• chr10-3011651-C-T
• rs10751904
• ENST00000439575.2:n.816C>T

Variant summary

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

The ENST00000439575.2(ENSG00000234182):​n.816C>T 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 0.269 in 149,446 control chromosomes in the GnomAD database, including 8,760 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 0.27 (8759 hom., cov: 28)
  • Exomes 𝑓: 0.21 (1 hom.)
• Consequence: ENSG00000234182 ENST00000439575.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 0 publications found

Genes affected

ENSG00000234182 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439575.2. 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
	ENSG00000234182	ENST00000439575.2	TSL:2	n.816C>T		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40108 AN: 149314 Hom.: 8730 Cov.: 28

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.243

GnomAD4 exome AF: 0.208 AC: 5 AN: 24 Hom.: 1 Cov.: 0 AF XY: 0.188 AC XY: 3 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 4 AN: 20

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.269 AC: 40184 AN: 149422 Hom.: 8759 Cov.: 28 AF XY: 0.263 AC XY: 19102 AN XY: 72700

African (AFR) AF: 0.608 AC: 24619 AN: 40476

American (AMR) AF: 0.176 AC: 2629 AN: 14932

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3460

East Asian (EAS) AF: 0.0608 AC: 309 AN: 5084

South Asian (SAS) AF: 0.187 AC: 880 AN: 4700

European-Finnish (FIN) AF: 0.111 AC: 1102 AN: 9952

Middle Eastern (MID) AF: 0.294 AC: 84 AN: 286

European-Non Finnish (NFE) AF: 0.136 AC: 9218 AN: 67572

Other (OTH) AF: 0.243 AC: 501 AN: 2062

Alfa AF: 0.211 Hom.: 734

Bravo AF: 0.287

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.47
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10751904; hg19: chr10-3053843;