rs12144971

chr1-221859143-C-T

Variant summary

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

The XR_007066885.1(LOC124904517):n.330+7078C>T 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 0.534 in 152,072 control chromosomes in the GnomAD database, including 22,083 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 0.53 (22083 hom., cov: 32)
• Consequence: LOC124904517 XR_007066885.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

Genes affected

LOC124904517 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904517	XR_007066885.1	n.330+7078C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81116 AN: 151954 Hom.: 22060 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.534 AC: 81191 AN: 152072 Hom.: 22083 Cov.: 32 AF XY: 0.531 AC XY: 39451 AN XY: 74322

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.527

Alfa AF: 0.568 Hom.: 38275

Bravo AF: 0.517

Asia WGS AF: 0.430 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	2.9
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12144971; hg19: chr1-222032485; COSMIC: COSV60032674;