rs4131535

chr12-94704012-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124902989 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902989	XR_007063412.1	n.7746A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.298

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.13
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131535; hg19: chr12-95097788;