chr3-135506407-T-G

Variant names:

• chr3-135506407-T-G
• rs11712655
• XR_001740926.1:n.229+9743A>C

Variant summary

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

The XR_001740926.1(LOC105374122):​n.229+9743A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,116 control chromosomes in the GnomAD database, including 5,311 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 0.25 (5311 hom., cov: 32)
• Consequence: LOC105374122 XR_001740926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478
• Publications: 8 publications found

Genes affected

LOC105374122 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37284 AN: 151998 Hom.: 5306 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.245 AC: 37308 AN: 152116 Hom.: 5311 Cov.: 32 AF XY: 0.251 AC XY: 18685 AN XY: 74344

African (AFR) AF: 0.125 AC: 5209 AN: 41514

American (AMR) AF: 0.329 AC: 5025 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3468

East Asian (EAS) AF: 0.519 AC: 2667 AN: 5142

South Asian (SAS) AF: 0.436 AC: 2102 AN: 4822

European-Finnish (FIN) AF: 0.224 AC: 2370 AN: 10568

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18211 AN: 67998

Other (OTH) AF: 0.263 AC: 555 AN: 2110

Alfa AF: 0.264 Hom.: 16146

Bravo AF: 0.245

Asia WGS AF: 0.459 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.44
DANN	Benign	0.29
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs11712655; hg19: chr3-135225249;