6-90902207-G-T

Variant summary

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

The XR_001744259.1(LOC107986623):n.1244-5849G>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 0.188 in 152,064 control chromosomes in the GnomAD database, including 2,877 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 0.19 (2877 hom., cov: 32)
• Consequence: LOC107986623 XR_001744259.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

Genes affected

LOC107986623 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986623	XR_001744259.1	n.1244-5849G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28567 AN: 151946 Hom.: 2870 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0350

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.188 AC: 28611 AN: 152064 Hom.: 2877 Cov.: 32 AF XY: 0.187 AC XY: 13930 AN XY: 74318

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0349

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.168

Alfa AF: 0.160 Hom.: 4082

Bravo AF: 0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.77
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12191179; hg19: chr6-91611925;