3-5969952-A-G

Variant names:

• chr3-5969952-A-G
• rs953402
• ENST00000425894.2:n.1010+6437A>G

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.1010+6437A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 151,980 control chromosomes in the GnomAD database, including 32,924 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 0.64 (32924 hom., cov: 31)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.902
• Publications: 3 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425894.2. 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
	ENSG00000229642	ENST00000425894.2	TSL:3	n.1010+6437A>G		intron	N/A
	ENSG00000229642	ENST00000779001.1		n.1157+6437A>G		intron	N/A
	ENSG00000229642	ENST00000779002.1		n.781+6437A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97254 AN: 151862 Hom.: 32925 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.640 AC: 97289 AN: 151980 Hom.: 32924 Cov.: 31 AF XY: 0.639 AC XY: 47426 AN XY: 74256

African (AFR) AF: 0.403 AC: 16699 AN: 41420

American (AMR) AF: 0.663 AC: 10116 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2837 AN: 3472

East Asian (EAS) AF: 0.675 AC: 3480 AN: 5154

South Asian (SAS) AF: 0.614 AC: 2956 AN: 4812

European-Finnish (FIN) AF: 0.762 AC: 8054 AN: 10566

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50792 AN: 67976

Other (OTH) AF: 0.650 AC: 1372 AN: 2110

Alfa AF: 0.717 Hom.: 24714

Bravo AF: 0.626

Asia WGS AF: 0.651 AC: 2263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.3
DANN	Benign	0.71
PhyloP100		0.90

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: rs953402;

hg19: chr3-6011639;