3-149225477-A-G

Variant summary

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

The ENST00000663884.1(ENSG00000286714):n.261+101A>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 0.195 in 152,100 control chromosomes in the GnomAD database, including 3,039 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 0.19 (3039 hom., cov: 32)
• Consequence: ENST00000663884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927942	XR_241588.4	n.529+101A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663884.1	n.261+101A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29594 AN: 151982 Hom.: 3030 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.195 AC: 29623 AN: 152100 Hom.: 3039 Cov.: 32 AF XY: 0.198 AC XY: 14743 AN XY: 74370

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.212

Alfa AF: 0.196 Hom.: 1444

Bravo AF: 0.192

Asia WGS AF: 0.272 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.9
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11708215; hg19: chr3-148943264;