rs1488407

chr3-3617882-G-C

Variant summary

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

The ENST00000420000.6(ENSG00000223727):n.200+8862C>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 0.134 in 152,146 control chromosomes in the GnomAD database, including 1,461 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 0.13 (1461 hom., cov: 33)
• Consequence: ENST00000420000.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.826

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 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.200+8862C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20384 AN: 152028 Hom.: 1457 Cov.: 33

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.134 AC: 20401 AN: 152146 Hom.: 1461 Cov.: 33 AF XY: 0.134 AC XY: 9984 AN XY: 74384

Gnomad4 AFR AF: 0.0845

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.127

Alfa AF: 0.140 Hom.: 200

Bravo AF: 0.129

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.1
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1488407; hg19: chr3-3659566;