rs13085623

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287421	ENST00000667697.1		n.255-9770T>G		intron	N/A
	ENSG00000308895	ENST00000837134.1		n.191+305A>C		intron	N/A
	ENSG00000308895	ENST00000837135.1		n.232+305A>C		intron	N/A

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

African (AFR) AF: 0.275 AC: 11429 AN: 41502

American (AMR) AF: 0.275 AC: 4199 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1171 AN: 5176

South Asian (SAS) AF: 0.361 AC: 1743 AN: 4822

European-Finnish (FIN) AF: 0.191 AC: 2022 AN: 10598

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17285 AN: 67952

Other (OTH) AF: 0.258 AC: 543 AN: 2108

Alfa AF: 0.261 Hom.: 3570

Bravo AF: 0.262

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.58
DANN	Benign	0.46
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs13085623; hg19: chr3-105932735;