chr7-12482533-C-A

Position:

• chr7-12482533-C-A

Variant summary

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

The XR_001745093.2(LOC105375156):​n.618-1546G>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 0.834 in 152,202 control chromosomes in the GnomAD database, including 53,334 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 0.83 (53334 hom., cov: 33)
• Consequence: LOC105375156 XR_001745093.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

LOC105375156 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375156	XR_001745093.2	n.618-1546G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641054.1	n.269-4431C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126891 AN: 152084 Hom.: 53274 Cov.: 33

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.834 AC: 127005 AN: 152202 Hom.: 53334 Cov.: 33 AF XY: 0.829 AC XY: 61703 AN XY: 74404

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.807

Alfa AF: 0.807 Hom.: 26632

Bravo AF: 0.846

Asia WGS AF: 0.803 AC: 2788 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs847936; hg19: chr7-12522159;