4-23343831-T-G

Variant names:

• chr4-23343831-T-G
• rs1396669
• ENST00000757640.1:n.285-14388A>C

Variant summary

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

The ENST00000757640.1(ENSG00000298732):​n.285-14388A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,910 control chromosomes in the GnomAD database, including 11,075 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 0.36 (11075 hom., cov: 33)
• Consequence: ENSG00000298732 ENST00000757640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523
• Publications: 4 publications found

Genes affected

ENSG00000298732 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757640.1. 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
	ENSG00000298732	ENST00000757640.1		n.285-14388A>C		intron	N/A
	ENSG00000298732	ENST00000757641.1		n.268-14388A>C		intron	N/A
	ENSG00000298732	ENST00000757642.1		n.253-14388A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54427 AN: 151792 Hom.: 11071 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.358 AC: 54441 AN: 151910 Hom.: 11075 Cov.: 33 AF XY: 0.361 AC XY: 26761 AN XY: 74220

African (AFR) AF: 0.147 AC: 6106 AN: 41490

American (AMR) AF: 0.446 AC: 6793 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3468

East Asian (EAS) AF: 0.465 AC: 2382 AN: 5124

South Asian (SAS) AF: 0.424 AC: 2046 AN: 4822

European-Finnish (FIN) AF: 0.425 AC: 4484 AN: 10560

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29594 AN: 67886

Other (OTH) AF: 0.375 AC: 792 AN: 2112

Alfa AF: 0.408 Hom.: 36308

Bravo AF: 0.350

Asia WGS AF: 0.434 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.57
PhyloP100		0.52

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: rs1396669;

hg19: chr4-23345454;