chr12-115774058-G-A

Variant names:

• chr12-115774058-G-A
• rs17719439
• ENST00000549163.1:n.292+8442G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000549163.1(ENSG00000257781):​n.292+8442G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.034 in 149,206 control chromosomes in the GnomAD database, including 109 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 0.034 (109 hom., cov: 31)
• Consequence: ENSG00000257781 ENST00000549163.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 2 publications found

Genes affected

ENSG00000257781 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.034 (5070/149206) while in subpopulation NFE AF = 0.0399 (2693/67574). AF 95% confidence interval is 0.0386. There are 109 homozygotes in GnomAd4. There are 2378 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 109 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549163.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257781	ENST00000549163.1	TSL:3	n.292+8442G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0340 AC: 5066 AN: 149144 Hom.: 108 Cov.: 31

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.0210

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0791

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00699

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0340 AC: 5070 AN: 149206 Hom.: 109 Cov.: 31 AF XY: 0.0328 AC XY: 2378 AN XY: 72560

African (AFR) AF: 0.0308 AC: 1249 AN: 40490

American (AMR) AF: 0.0355 AC: 533 AN: 15024

Ashkenazi Jewish (ASJ) AF: 0.0791 AC: 274 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5024

South Asian (SAS) AF: 0.00701 AC: 33 AN: 4706

European-Finnish (FIN) AF: 0.0164 AC: 159 AN: 9682

Middle Eastern (MID) AF: 0.0571 AC: 16 AN: 280

European-Non Finnish (NFE) AF: 0.0399 AC: 2693 AN: 67574

Other (OTH) AF: 0.0457 AC: 94 AN: 2058

Alfa AF: 0.0398 Hom.: 227

Bravo AF: 0.0362

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.36
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs17719439; hg19: chr12-116211863;