rs12666416

chr7-12002791-A-Gchr7-12002791-A-T

Variant summary

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

The XR_007060211.1(LOC124901589):n.85+91862T>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 0.483 in 151,818 control chromosomes in the GnomAD database, including 18,099 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 0.48 (18099 hom., cov: 32)
• Consequence: LOC124901589 XR_007060211.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

Genes affected

LOC124901589 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901589	XR_007060211.1	n.85+91862T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73350 AN: 151698 Hom.: 18090 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.483 AC: 73390 AN: 151818 Hom.: 18099 Cov.: 32 AF XY: 0.490 AC XY: 36330 AN XY: 74166

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.484

Alfa AF: 0.469 Hom.: 13310

Bravo AF: 0.475

Asia WGS AF: 0.674 AC: 2338 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.92
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12666416; hg19: chr7-12042417;