ENST00000821810.1:n.793-10670A>C

Variant names:

• chr10-9209716-T-G
• rs1242969
• ENST00000821810.1:n.793-10670A>C

Variant summary

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

The ENST00000821810.1(ENSG00000306888):​n.793-10670A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,032 control chromosomes in the GnomAD database, including 6,268 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 0.27 (6268 hom., cov: 32)
• Consequence: ENSG00000306888 ENST00000821810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 1 publications found

Genes affected

ENSG00000306888 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928272	NR_120635.1	n.590-10670A>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306888	ENST00000821810.1	n.793-10670A>C		intron_variant	Intron 2 of 2
ENSG00000306888	ENST00000821811.1	n.424-10670A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40676 AN: 151912 Hom.: 6273 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.267 AC: 40667 AN: 152032 Hom.: 6268 Cov.: 32 AF XY: 0.271 AC XY: 20173 AN XY: 74320

African (AFR) AF: 0.120 AC: 4964 AN: 41488

American (AMR) AF: 0.268 AC: 4096 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3468

East Asian (EAS) AF: 0.390 AC: 2010 AN: 5152

South Asian (SAS) AF: 0.468 AC: 2256 AN: 4824

European-Finnish (FIN) AF: 0.340 AC: 3591 AN: 10566

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.325 AC: 22068 AN: 67940

Other (OTH) AF: 0.284 AC: 598 AN: 2108

Alfa AF: 0.302 Hom.: 7418

Bravo AF: 0.251

Asia WGS AF: 0.407 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
DANN	Benign	0.26
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1242969; hg19: chr10-9251679;