rs7302032

chr12-5246207-G-Achr12-5246207-G-C

Variant summary

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

The XR_931577.2(LOC105369617):n.769-23998G>A 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 0.0848 in 152,054 control chromosomes in the GnomAD database, including 724 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 0.085 (724 hom., cov: 32)
• Consequence: LOC105369617 XR_931577.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604

Genes affected

LOC105369617 (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 (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369617	XR_931577.2	n.769-23998G>A		intron_variant, non_coding_transcript_variant
LOC105369617	XR_001748970.2	n.742-23998G>A		intron_variant, non_coding_transcript_variant
LOC105369617	XR_007063177.1	n.716-23998G>A		intron_variant, non_coding_transcript_variant
LOC105369617	XR_007063178.1	n.725-23998G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0847 AC: 12875 AN: 151936 Hom.: 722 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.0479

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0687

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

GnomAD4 genome AF: 0.0848 AC: 12891 AN: 152054 Hom.: 724 Cov.: 32 AF XY: 0.0818 AC XY: 6080 AN XY: 74336

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0460

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0565

Gnomad4 FIN AF: 0.0479

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.0680

Alfa AF: 0.0649 Hom.: 480

Bravo AF: 0.0875

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.75
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7302032; hg19: chr12-5355373;