rs12142165

chr1-228195501-T-Cchr1-228195501-T-G

Variant summary

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

The XR_007066917.1(LOC124904536):n.7072+734T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,042 control chromosomes in the GnomAD database, including 7,314 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 0.30 (7314 hom., cov: 32)
• Consequence: LOC124904536 XR_007066917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474

Genes affected

LOC124904536 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904536	XR_007066917.1	n.7072+734T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44909 AN: 151922 Hom.: 7311 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.295 AC: 44914 AN: 152042 Hom.: 7314 Cov.: 32 AF XY: 0.295 AC XY: 21961 AN XY: 74328

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.319

Alfa AF: 0.352 Hom.: 18093

Bravo AF: 0.290

Asia WGS AF: 0.441 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.9
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12142165; hg19: chr1-228383202;