rs963130

Variant names:

• chr3-3474738-T-C
• rs963130
• ENST00000420000.6:n.201-92088A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000455703.1(ENSG00000223727):​n.59+9301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0345 in 151,982 control chromosomes in the GnomAD database, including 510 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 0.034 (510 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000455703.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223727	ENST00000420000.6	n.201-92088A>G		intron_variant	Intron 2 of 4	4
ENSG00000223727	ENST00000451031.5	n.77+9301A>G		intron_variant	Intron 1 of 5	3
ENSG00000223727	ENST00000455703.1	n.59+9301A>G		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.0345 AC: 5243 AN: 151864 Hom.: 513 Cov.: 32

Gnomad AFR AF: 0.00582

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0724

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0700

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00823

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0345 AC: 5239 AN: 151982 Hom.: 510 Cov.: 32 AF XY: 0.0414 AC XY: 3072 AN XY: 74290

Gnomad4 AFR AF: 0.00580

Gnomad4 AMR AF: 0.0724

Gnomad4 ASJ AF: 0.0136

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0700

Gnomad4 NFE AF: 0.00824

Gnomad4 OTH AF: 0.0265

Alfa AF: 0.0178 Hom.: 16

Bravo AF: 0.0330

Asia WGS AF: 0.221 AC: 766 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs963130; hg19: chr3-3516422;