rs17719439

Positions:

• chr12-115774058-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000549163.1(ENSG00000257781):​n.292+8442G>A variant causes a intron, non coding transcript 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: ENST00000549163.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 109 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000549163.1	n.292+8442G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0308

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.0791

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00701

Gnomad4 FIN AF: 0.0164

Gnomad4 NFE AF: 0.0399

Gnomad4 OTH AF: 0.0457

Alfa AF: 0.0401 Hom.: 187

Bravo AF: 0.0362

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17719439; hg19: chr12-116211863;