rs1024612

Variant names:

• chr17-34222337-A-G
• rs1024612
• ENST00000776537.1:n.239-2916T>C

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.239-2916T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 152,072 control chromosomes in the GnomAD database, including 29,466 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 0.62 (29466 hom., cov: 32)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 11 publications found

Genes affected

ENSG00000301139 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 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
ENSG00000301139	ENST00000776537.1	n.239-2916T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93827 AN: 151954 Hom.: 29442 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.617 AC: 93899 AN: 152072 Hom.: 29466 Cov.: 32 AF XY: 0.628 AC XY: 46696 AN XY: 74316

African (AFR) AF: 0.573 AC: 23731 AN: 41444

American (AMR) AF: 0.717 AC: 10954 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2118 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4438 AN: 5168

South Asian (SAS) AF: 0.817 AC: 3948 AN: 4832

European-Finnish (FIN) AF: 0.630 AC: 6650 AN: 10558

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.589 AC: 40074 AN: 68000

Other (OTH) AF: 0.630 AC: 1331 AN: 2112

Alfa AF: 0.610 Hom.: 5337

Bravo AF: 0.618

Asia WGS AF: 0.824 AC: 2863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1024612; hg19: chr17-32549356;