3-178123979-A-G

Position:

• chr3-178123979-A-G

Variant summary

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

The ENST00000651726.1(ENSG00000286003):​n.234+48237T>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 0.435 in 152,010 control chromosomes in the GnomAD database, including 15,081 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 0.44 (15081 hom., cov: 32)
• Consequence: ENST00000651726.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 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
	ENST00000651726.1	n.234+48237T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66154 AN: 151894 Hom.: 15072 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.435 AC: 66190 AN: 152010 Hom.: 15081 Cov.: 32 AF XY: 0.441 AC XY: 32738 AN XY: 74318

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.445

Alfa AF: 0.418 Hom.: 2216

Bravo AF: 0.435

Asia WGS AF: 0.594 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725318; hg19: chr3-177841767;