rs10849023

Variant names:

• chr12-4223312-C-T
• rs10849023
• ENST00000753113.1:n.474G>A

Variant summary

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

The ENST00000753113.1(ENSG00000298123):​n.474G>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 0.219 in 152,170 control chromosomes in the GnomAD database, including 3,765 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 (3765 hom., cov: 33)
• Consequence: ENSG00000298123 ENST00000753113.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 24 publications found

Genes affected

ENSG00000298123 (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 = 0.233 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
ENSG00000298123	ENST00000753113.1	n.474G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000298123	ENST00000753114.1	n.451G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000298123	ENST00000753115.1	n.448G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33304 AN: 152052 Hom.: 3759 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.219 AC: 33350 AN: 152170 Hom.: 3765 Cov.: 33 AF XY: 0.221 AC XY: 16420 AN XY: 74402

African (AFR) AF: 0.237 AC: 9843 AN: 41514

American (AMR) AF: 0.222 AC: 3393 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1193 AN: 5170

South Asian (SAS) AF: 0.148 AC: 715 AN: 4824

European-Finnish (FIN) AF: 0.226 AC: 2386 AN: 10576

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

European-Non Finnish (NFE) AF: 0.211 AC: 14324 AN: 68002

Other (OTH) AF: 0.232 AC: 491 AN: 2114

Alfa AF: 0.215 Hom.: 14455

Bravo AF: 0.221

Asia WGS AF: 0.193 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.70
DANN	Benign	0.72
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10849023; hg19: chr12-4332478;