rs10841397

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

ENSG00000255910 (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 (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000535764.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255910	ENST00000535764.1	TSL:3	n.154-12164T>C		intron	N/A
	ENSG00000255910	ENST00000716354.1		n.257-12164T>C		intron	N/A
	ENSG00000255910	ENST00000716355.1		n.187-12164T>C		intron	N/A

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

African (AFR) AF: 0.234 AC: 9700 AN: 41466

American (AMR) AF: 0.314 AC: 4802 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1398 AN: 3468

East Asian (EAS) AF: 0.119 AC: 614 AN: 5178

South Asian (SAS) AF: 0.292 AC: 1410 AN: 4824

European-Finnish (FIN) AF: 0.256 AC: 2707 AN: 10588

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 27014 AN: 67980

Other (OTH) AF: 0.357 AC: 752 AN: 2108

Alfa AF: 0.375 Hom.: 35376

Bravo AF: 0.322

Asia WGS AF: 0.217 AC: 755 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.79
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10841397; hg19: chr12-20063968;