chr12-104774653-A-T

Variant names:

• chr12-104774653-A-T
• rs2463021
• ENST00000839921.1:n.199+9823A>T

Variant summary

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

The ENST00000839921.1(ENSG00000309266):​n.199+9823A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 152,268 control chromosomes in the GnomAD database, including 619 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 0.078 (619 hom., cov: 32)
• Consequence: ENSG00000309266 ENST00000839921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 2 publications found

Genes affected

ENSG00000309266 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 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
ENSG00000309266	ENST00000839921.1	n.199+9823A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11826 AN: 152150 Hom.: 619 Cov.: 32

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0777 AC: 11831 AN: 152268 Hom.: 619 Cov.: 32 AF XY: 0.0735 AC XY: 5474 AN XY: 74456

African (AFR) AF: 0.0314 AC: 1303 AN: 41558

American (AMR) AF: 0.0841 AC: 1286 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5188

South Asian (SAS) AF: 0.0514 AC: 248 AN: 4828

European-Finnish (FIN) AF: 0.0287 AC: 305 AN: 10620

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7616 AN: 67992

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.0349 Hom.: 30

Bravo AF: 0.0814

Asia WGS AF: 0.0300 AC: 102 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.73
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2463021; hg19: chr12-105168431;