rs10841397

Variant names:

• chr12-19911034-T-C
• rs10841397
• ENST00000535764.1:n.154-12164T>C

Variant summary

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

The ENST00000535764.1(ENSG00000255910):​n.154-12164T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,094 control chromosomes in the GnomAD database, including 8,522 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 0.32 (8522 hom., cov: 33)
• Consequence: ENSG00000255910 ENST00000535764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

ENSG00000255910 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 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
ENSG00000255910	ENST00000535764.1	n.154-12164T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.322 AC: 49005 AN: 151976 Hom.: 8528 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.322 AC: 48994 AN: 152094 Hom.: 8522 Cov.: 33 AF XY: 0.315 AC XY: 23398 AN XY: 74354

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.357

Alfa AF: 0.391 Hom.: 14379

Bravo AF: 0.322

Asia WGS AF: 0.217 AC: 755 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10841397; hg19: chr12-20063968;