ENST00000535764.1:n.212+9470T>C

Variant names:

• chr12-19932726-T-C
• rs10505845
• ENST00000535764.1:n.212+9470T>C

Variant summary

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

The ENST00000535764.1(ENSG00000255910):​n.212+9470T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,068 control chromosomes in the GnomAD database, including 9,095 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 0.34 (9095 hom., cov: 33)
• Consequence: ENSG00000255910 ENST00000535764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255910	ENST00000535764.1	TSL:3	n.212+9470T>C		intron	N/A
	ENSG00000255910	ENST00000716354.1		n.315+9470T>C		intron	N/A
	ENSG00000255910	ENST00000716355.1		n.245+9470T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51141 AN: 151948 Hom.: 9073 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.337 AC: 51210 AN: 152068 Hom.: 9095 Cov.: 33 AF XY: 0.335 AC XY: 24932 AN XY: 74340

African (AFR) AF: 0.393 AC: 16311 AN: 41468

American (AMR) AF: 0.365 AC: 5573 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3470

East Asian (EAS) AF: 0.635 AC: 3275 AN: 5160

South Asian (SAS) AF: 0.194 AC: 934 AN: 4824

European-Finnish (FIN) AF: 0.253 AC: 2676 AN: 10580

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20262 AN: 67984

Other (OTH) AF: 0.347 AC: 730 AN: 2106

Alfa AF: 0.320 Hom.: 15752

Bravo AF: 0.353

Asia WGS AF: 0.361 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.63
PhyloP100		0.65

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10505845;

hg19: chr12-20085660;