3-149225477-A-G

Variant names:

• chr3-149225477-A-G
• rs11708215
• ENST00000790430.1:n.674A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000790430.1(ENSG00000286714):​n.674A>G variant causes a non coding transcript exon 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: ENSG00000286714 ENST00000790430.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 10 publications found

Genes affected

ENSG00000286714 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC101927942	XR_241588.4	n.529+101A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286714	ENST00000790430.1	n.674A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000286714	ENST00000663884.2	n.309+101A>G		intron_variant	Intron 3 of 3
ENSG00000286714	ENST00000790417.1	n.61+101A>G		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.149 AC: 6159 AN: 41472

American (AMR) AF: 0.213 AC: 3257 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1697 AN: 5160

South Asian (SAS) AF: 0.222 AC: 1065 AN: 4808

European-Finnish (FIN) AF: 0.243 AC: 2572 AN: 10578

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13630 AN: 68002

Other (OTH) AF: 0.212 AC: 448 AN: 2116

Alfa AF: 0.196 Hom.: 1602

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs11708215; hg19: chr3-148943264;