chr3-106213888-T-G

Variant names:

• chr3-106213888-T-G
• rs13085623
• ENST00000667697.1:n.255-9770T>G

Variant summary

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

The ENST00000667697.1(ENSG00000287421):​n.255-9770T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,094 control chromosomes in the GnomAD database, including 5,263 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 (5263 hom., cov: 32)
• Consequence: ENSG00000287421 ENST00000667697.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555

Genes affected

ENSG00000287421 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287421	ENST00000667697.1	n.255-9770T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39362 AN: 151976 Hom.: 5235 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.259 AC: 39453 AN: 152094 Hom.: 5263 Cov.: 32 AF XY: 0.260 AC XY: 19337 AN XY: 74360

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.258

Alfa AF: 0.265 Hom.: 2753

Bravo AF: 0.262

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.58
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13085623; hg19: chr3-105932735;