7-9788878-C-T

Variant summary

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

The XR_927026.2(LOC105375147):n.210-28815G>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 0.577 in 151,748 control chromosomes in the GnomAD database, including 25,579 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 0.58 (25579 hom., cov: 30)
• Consequence: LOC105375147 XR_927026.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

LOC105375147 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375147	XR_927026.2	n.210-28815G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87538 AN: 151630 Hom.: 25571 Cov.: 30

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.577 AC: 87584 AN: 151748 Hom.: 25579 Cov.: 30 AF XY: 0.576 AC XY: 42714 AN XY: 74162

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.542

Alfa AF: 0.570 Hom.: 18299

Bravo AF: 0.568

Asia WGS AF: 0.587 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.37
Dann	Benign	0.071

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12667020; hg19: chr7-9828507;