rs10842853

chr12-27107481-T-Cchr12-27107481-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000538920.1(ENSG00000256226):n.244-2223A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0916 in 152,270 control chromosomes in the GnomAD database, including 810 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 0.092 (810 hom., cov: 32)
• Consequence: ENST00000538920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000538920.1	n.244-2223A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13957 AN: 152152 Hom.: 810 Cov.: 32

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0286

Gnomad SAS AF: 0.0571

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.0881

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

GnomAD4 genome AF: 0.0916 AC: 13955 AN: 152270 Hom.: 810 Cov.: 32 AF XY: 0.0906 AC XY: 6742 AN XY: 74450

Gnomad4 AFR AF: 0.0221

Gnomad4 AMR AF: 0.0868

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0287

Gnomad4 SAS AF: 0.0571

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.0882

Alfa AF: 0.0673 Hom.: 123

Bravo AF: 0.0863

Asia WGS AF: 0.0440 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.0
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10842853; hg19: chr12-27260414;