rs4131535

Variant names:

• chr12-94704012-T-C
• rs4131535
• XR_007063412.1:n.7746A>G

Variant summary

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

The XR_007063412.1(LOC124902989):​n.7746A>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 0.291 in 152,130 control chromosomes in the GnomAD database, including 6,435 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 0.29 (6435 hom., cov: 32)
• Consequence: LOC124902989 XR_007063412.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 4 publications found

Genes affected

LOC124902989 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44200 AN: 152012 Hom.: 6432 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.291 AC: 44233 AN: 152130 Hom.: 6435 Cov.: 32 AF XY: 0.290 AC XY: 21601 AN XY: 74374

African (AFR) AF: 0.275 AC: 11397 AN: 41500

American (AMR) AF: 0.275 AC: 4205 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 970 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1262 AN: 5186

South Asian (SAS) AF: 0.341 AC: 1645 AN: 4826

European-Finnish (FIN) AF: 0.306 AC: 3236 AN: 10564

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

European-Non Finnish (NFE) AF: 0.303 AC: 20608 AN: 67990

Other (OTH) AF: 0.298 AC: 630 AN: 2114

Alfa AF: 0.290 Hom.: 1111

Bravo AF: 0.287

Asia WGS AF: 0.298 AC: 1035 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.43
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4131535; hg19: chr12-95097788;