rs7800391

chr7-110568186-C-T

Variant summary

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

The XR_927864.3(LOC105375452):n.239-3487C>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 0.328 in 151,750 control chromosomes in the GnomAD database, including 10,056 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 0.33 (10056 hom., cov: 30)
• Consequence: LOC105375452 XR_927864.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

Genes affected

LOC105375452 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375452	XR_927864.3	n.239-3487C>T		intron_variant, non_coding_transcript_variant
LOC105375452	XR_927865.3	n.239-3487C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49785 AN: 151636 Hom.: 10050 Cov.: 30

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.328 AC: 49788 AN: 151750 Hom.: 10056 Cov.: 30 AF XY: 0.330 AC XY: 24499 AN XY: 74172

Gnomad4 AFR AF: 0.0821

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.327

Alfa AF: 0.414 Hom.: 17735

Bravo AF: 0.317

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.2
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7800391; hg19: chr7-110208243;