chr3-178075319-G-T

Position:

• chr3-178075319-G-T

Variant summary

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

The ENST00000651726.1(ENSG00000286003):​n.235-44414C>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 0.234 in 152,028 control chromosomes in the GnomAD database, including 5,134 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 0.23 (5134 hom., cov: 32)
• Consequence: ENST00000651726.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.757

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651726.1	n.235-44414C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35529 AN: 151910 Hom.: 5112 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.234 AC: 35580 AN: 152028 Hom.: 5134 Cov.: 32 AF XY: 0.244 AC XY: 18156 AN XY: 74298

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.263

Alfa AF: 0.225 Hom.: 5990

Bravo AF: 0.236

Asia WGS AF: 0.523 AC: 1815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1982821; hg19: chr3-177793107;