chr3-120866468-C-T

Position:

• chr3-120866468-C-T

Variant summary

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

The ENST00000658056.1(ENSG00000287366):​n.432-5224C>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 0.386 in 151,946 control chromosomes in the GnomAD database, including 11,546 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 0.39 (11546 hom., cov: 32)
• Consequence: ENST00000658056.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374069	XR_924399.4	n.429+1801G>A		intron_variant, non_coding_transcript_variant
LOC105374069	XR_924398.4	n.912+1801G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658056.1	n.432-5224C>T		intron_variant, non_coding_transcript_variant
	ENST00000661060.1	n.912+1801G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58670 AN: 151828 Hom.: 11543 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.386 AC: 58702 AN: 151946 Hom.: 11546 Cov.: 32 AF XY: 0.378 AC XY: 28094 AN XY: 74240

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.381

Alfa AF: 0.380 Hom.: 18209

Bravo AF: 0.393

Asia WGS AF: 0.218 AC: 759 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs322458; hg19: chr3-120585315;