6-155812936-C-T

Variant summary

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

The XR_001744423.2(LOC101928923):n.699-897G>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 0.123 in 152,002 control chromosomes in the GnomAD database, including 1,229 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 0.12 (1229 hom., cov: 31)
• Consequence: LOC101928923 XR_001744423.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

Genes affected

LOC101928923 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928923	XR_001744423.2	n.699-897G>A		intron_variant, non_coding_transcript_variant
LOC105378072	XR_001744424.2	n.79+19517C>T		intron_variant, non_coding_transcript_variant
LOC105378072	XR_007059824.1	n.79+19517C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18623 AN: 151884 Hom.: 1225 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0556

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.123 AC: 18649 AN: 152002 Hom.: 1229 Cov.: 31 AF XY: 0.122 AC XY: 9040 AN XY: 74288

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0555

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.116

Alfa AF: 0.127 Hom.: 595

Bravo AF: 0.125

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.78
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499298; hg19: chr6-156134070;