rs2032350

Variant names:

• chr4-99392905-C-T
• rs2032350
• ENST00000762194.1:n.378-9285G>A

Variant summary

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

The ENST00000762194.1(ENSG00000299279):​n.378-9285G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,768 control chromosomes in the GnomAD database, including 5,444 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 0.25 (5444 hom., cov: 32)
• Consequence: ENSG00000299279 ENST00000762194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 1 publications found

Genes affected

ENSG00000299279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762194.1. 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
	ENSG00000299279	ENST00000762194.1		n.378-9285G>A		intron	N/A
	ENSG00000299279	ENST00000762195.1		n.250-9285G>A		intron	N/A
	ENSG00000299279	ENST00000762196.1		n.493-9285G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37622 AN: 151650 Hom.: 5438 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.248 AC: 37652 AN: 151768 Hom.: 5444 Cov.: 32 AF XY: 0.255 AC XY: 18928 AN XY: 74170

African (AFR) AF: 0.301 AC: 12456 AN: 41370

American (AMR) AF: 0.181 AC: 2754 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3468

East Asian (EAS) AF: 0.676 AC: 3501 AN: 5182

South Asian (SAS) AF: 0.467 AC: 2244 AN: 4806

European-Finnish (FIN) AF: 0.172 AC: 1808 AN: 10496

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13513 AN: 67904

Other (OTH) AF: 0.233 AC: 489 AN: 2098

Alfa AF: 0.225 Hom.: 555

Bravo AF: 0.247

Asia WGS AF: 0.467 AC: 1616 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.57
PhyloP100		0.14

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: rs2032350;

hg19: chr4-100314062;