rs1012919

Variant names:

• chr14-35415433-T-G
• rs1012919
• ENST00000848537.1:n.241+12046T>G

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.241+12046T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,134 control chromosomes in the GnomAD database, including 39,918 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 0.72 (39918 hom., cov: 33)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 6 publications found

Genes affected

ENSG00000310246 (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 (AFR) allele frequency at 95% confidence interval = 0.795 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
ENSG00000310246	ENST00000848537.1	n.241+12046T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109753 AN: 152016 Hom.: 39852 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.722 AC: 109876 AN: 152134 Hom.: 39918 Cov.: 33 AF XY: 0.725 AC XY: 53901 AN XY: 74378

African (AFR) AF: 0.802 AC: 33290 AN: 41504

American (AMR) AF: 0.776 AC: 11869 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2439 AN: 3472

East Asian (EAS) AF: 0.739 AC: 3827 AN: 5182

South Asian (SAS) AF: 0.732 AC: 3531 AN: 4822

European-Finnish (FIN) AF: 0.728 AC: 7690 AN: 10560

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.663 AC: 45085 AN: 67990

Other (OTH) AF: 0.705 AC: 1486 AN: 2108

Alfa AF: 0.682 Hom.: 149471

Bravo AF: 0.729

Asia WGS AF: 0.773 AC: 2686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.60
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1012919; hg19: chr14-35884639;