rs1321632

Variant names:

• chr3-197365786-C-T
• rs1321632
• ENST00000794352.1:n.264-19355G>A

Variant summary

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

The ENST00000794352.1(ENSG00000235126):​n.264-19355G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,134 control chromosomes in the GnomAD database, including 1,761 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 0.13 (1761 hom., cov: 32)
• Consequence: ENSG00000235126 ENST00000794352.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 2 publications found

Genes affected

ENSG00000235126 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794352.1. 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
	ENSG00000235126	ENST00000794352.1		n.264-19355G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19497 AN: 152016 Hom.: 1758 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0526

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.128 AC: 19522 AN: 152134 Hom.: 1761 Cov.: 32 AF XY: 0.127 AC XY: 9422 AN XY: 74392

African (AFR) AF: 0.259 AC: 10726 AN: 41444

American (AMR) AF: 0.0927 AC: 1418 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3468

East Asian (EAS) AF: 0.0526 AC: 272 AN: 5176

South Asian (SAS) AF: 0.135 AC: 648 AN: 4816

European-Finnish (FIN) AF: 0.0600 AC: 637 AN: 10612

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.0763 AC: 5186 AN: 68006

Other (OTH) AF: 0.121 AC: 256 AN: 2114

Alfa AF: 0.0921 Hom.: 3216

Bravo AF: 0.134

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.65
PhyloP100		1.2

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: rs1321632;

hg19: chr3-197092657;