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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723596	XR_001740591.3	n.632+6437A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229642	ENST00000425894.2	n.1010+6437A>G		intron_variant	Intron 6 of 8	3
ENSG00000229642	ENST00000779001.1	n.1157+6437A>G		intron_variant	Intron 6 of 7
ENSG00000229642	ENST00000779002.1	n.781+6437A>G		intron_variant	Intron 5 of 7

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 v4.3

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

Other links and lift over

dbSNP: rs953402; hg19: chr3-6011639;