rs963130

chr3-3474738-T-C

Variant summary

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

The ENST00000420000.6(ENSG00000223727):n.201-92088A>G variant causes a intron, non coding transcript 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: ENST00000420000.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000420000.6	n.201-92088A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000451031.5	n.77+9301A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000455703.1	n.59+9301A>G		intron_variant, non_coding_transcript_variant		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;