3-19638916-C-T

Variant names:

• chr3-19638916-C-T
• rs2203428
• ENST00000670571.1:n.512-22863G>A

Variant summary

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

The ENST00000670571.1(ENSG00000287069):​n.512-22863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,904 control chromosomes in the GnomAD database, including 4,052 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 0.18 (4052 hom., cov: 32)
• Consequence: ENSG00000287069 ENST00000670571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 2 publications found

Genes affected

ENSG00000287069 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670571.1. 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
	ENSG00000287069	ENST00000670571.1		n.512-22863G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28037 AN: 151786 Hom.: 4040 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.185 AC: 28095 AN: 151904 Hom.: 4052 Cov.: 32 AF XY: 0.185 AC XY: 13704 AN XY: 74250

African (AFR) AF: 0.389 AC: 16114 AN: 41390

American (AMR) AF: 0.169 AC: 2581 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0980 AC: 340 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1655 AN: 5140

South Asian (SAS) AF: 0.111 AC: 534 AN: 4822

European-Finnish (FIN) AF: 0.0701 AC: 741 AN: 10578

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0831 AC: 5645 AN: 67960

Other (OTH) AF: 0.175 AC: 369 AN: 2108

Alfa AF: 0.102 Hom.: 656

Bravo AF: 0.204

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		0.033

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: rs2203428;

hg19: chr3-19680408;