3-157975812-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651134.1(ENSG00000242536):n.570-13747G>C 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 0.411 in 151,470 control chromosomes in the GnomAD database, including 13,094 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 0.41 (13094 hom., cov: 31)
• Consequence: ENST00000651134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651134.1	n.570-13747G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62280 AN: 151348 Hom.: 13082 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.411 AC: 62328 AN: 151470 Hom.: 13094 Cov.: 31 AF XY: 0.411 AC XY: 30435 AN XY: 74008

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.409

Alfa AF: 0.301 Hom.: 780

Bravo AF: 0.404

Asia WGS AF: 0.507 AC: 1764 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	0.17
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9856195; hg19: chr3-157693601;