6-7431526-C-T

Variant summary

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

The XR_926434.2(LOC102724234):n.151+1389C>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 0.103 in 152,230 control chromosomes in the GnomAD database, including 1,174 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 0.10 (1174 hom., cov: 32)
• Consequence: LOC102724234 XR_926434.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

LOC102724234 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724234	XR_926434.2	n.151+1389C>T		intron_variant, non_coding_transcript_variant
LOC102724234	XR_427872.3	n.151+1389C>T		intron_variant, non_coding_transcript_variant
LOC102724234	XR_926435.2	n.151+1389C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15729 AN: 152112 Hom.: 1174 Cov.: 32

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.103 AC: 15727 AN: 152230 Hom.: 1174 Cov.: 32 AF XY: 0.110 AC XY: 8165 AN XY: 74414

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0957

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0979 Hom.: 374

Bravo AF: 0.106

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.24
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9379104; hg19: chr6-7431759;