3-180201290-T-C

Variant names:

• chr3-180201290-T-C
• rs4854964
• ENST00000765870.1:n.210-10840T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000765870.1(ENSG00000299725):​n.210-10840T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,984 control chromosomes in the GnomAD database, including 10,359 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 0.35 (10359 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000299725 ENST00000765870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 5 publications found

Genes affected

ENSG00000299725 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765870.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299725	ENST00000765870.1		n.210-10840T>C		intron	N/A
	ENSG00000299725	ENST00000765871.1		n.118+3364T>C		intron	N/A
	ENSG00000282327	ENST00000633048.1	TSL:6	n.*78T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52522 AN: 151866 Hom.: 10331 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.346 AC: 52602 AN: 151984 Hom.: 10359 Cov.: 32 AF XY: 0.351 AC XY: 26093 AN XY: 74328

African (AFR) AF: 0.532 AC: 22038 AN: 41406

American (AMR) AF: 0.375 AC: 5725 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3466

East Asian (EAS) AF: 0.381 AC: 1962 AN: 5144

South Asian (SAS) AF: 0.479 AC: 2307 AN: 4816

European-Finnish (FIN) AF: 0.249 AC: 2638 AN: 10580

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16137 AN: 67980

Other (OTH) AF: 0.331 AC: 698 AN: 2110

Alfa AF: 0.274 Hom.: 19768

Bravo AF: 0.359

Asia WGS AF: 0.457 AC: 1588 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.27

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4854964;

hg19: chr3-179919078;