3-106199811-G-A

Variant names:

• chr3-106199811-G-A
• rs12497363
• ENST00000667697.1:n.185-2703G>A

Variant summary

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

The ENST00000667697.1(ENSG00000287421):​n.185-2703G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,036 control chromosomes in the GnomAD database, including 5,092 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 0.26 (5092 hom., cov: 32)
• Consequence: ENSG00000287421 ENST00000667697.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 5 publications found

Genes affected

ENSG00000287421 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667697.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287421	ENST00000667697.1		n.185-2703G>A		intron	N/A
	ENSG00000287421	ENST00000837046.1		n.195-2703G>A		intron	N/A
	ENSG00000308895	ENST00000837134.1		n.232+9272C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38821 AN: 151916 Hom.: 5069 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.256 AC: 38903 AN: 152036 Hom.: 5092 Cov.: 32 AF XY: 0.257 AC XY: 19078 AN XY: 74324

African (AFR) AF: 0.262 AC: 10862 AN: 41414

American (AMR) AF: 0.275 AC: 4199 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1149 AN: 5184

South Asian (SAS) AF: 0.362 AC: 1747 AN: 4824

European-Finnish (FIN) AF: 0.193 AC: 2036 AN: 10556

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17316 AN: 67980

Other (OTH) AF: 0.255 AC: 539 AN: 2114

Alfa AF: 0.260 Hom.: 841

Bravo AF: 0.258

Asia WGS AF: 0.346 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.66
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs12497363; hg19: chr3-105918658;