3-120852757-C-T

Position:

• chr3-120852757-C-T

Variant summary

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

The ENST00000658056.1(ENSG00000287366):​n.228-1848C>T 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 0.309 in 152,070 control chromosomes in the GnomAD database, including 8,002 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 0.31 (8002 hom., cov: 32)
• Consequence: ENST00000658056.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 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
	ENST00000658056.1	n.228-1848C>T		intron_variant, non_coding_transcript_variant
	ENST00000661060.1	n.946+11803G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46920 AN: 151950 Hom.: 7990 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.309 AC: 46974 AN: 152070 Hom.: 8002 Cov.: 32 AF XY: 0.304 AC XY: 22621 AN XY: 74336

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.0158

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.301

Alfa AF: 0.285 Hom.: 1133

Bravo AF: 0.309

Asia WGS AF: 0.113 AC: 395 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2171168; hg19: chr3-120571604; COSMIC: COSV69482919;