10-111118043-G-C

Variant names:

• chr10-111118043-G-C
• rs2065779
• ENST00000812873.1:n.227G>C

Variant summary

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

The ENST00000812873.1(ENSG00000305773):​n.227G>C 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 0.22 in 152,182 control chromosomes in the GnomAD database, including 5,321 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 0.22 (5321 hom., cov: 33)
• Consequence: ENSG00000305773 ENST00000812873.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 5 publications found

Genes affected

ENSG00000305773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HEAT2	NR_159949.1	n.338G>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305773	ENST00000812873.1	n.227G>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000305773	ENST00000812874.1	n.343G>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33488 AN: 152064 Hom.: 5319 Cov.: 33

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.0853

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.220

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.220 AC: 33502 AN: 152182 Hom.: 5321 Cov.: 33 AF XY: 0.222 AC XY: 16503 AN XY: 74396

African (AFR) AF: 0.412 AC: 17078 AN: 41488

American (AMR) AF: 0.216 AC: 3301 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 489 AN: 3472

East Asian (EAS) AF: 0.465 AC: 2410 AN: 5178

South Asian (SAS) AF: 0.341 AC: 1642 AN: 4816

European-Finnish (FIN) AF: 0.0853 AC: 905 AN: 10612

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7068 AN: 68014

Other (OTH) AF: 0.224 AC: 474 AN: 2114

Alfa AF: 0.120 Hom.: 982

Bravo AF: 0.242

Asia WGS AF: 0.412 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	15
DANN	Benign	0.70
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2065779; hg19: chr10-112877801;