6-155850714-T-G

Position:

• chr6-155850714-T-G

Variant summary

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

The XR_001744423.2(LOC101928923):​n.406-17820A>C 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 0.0658 in 152,222 control chromosomes in the GnomAD database, including 493 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 0.066 (493 hom., cov: 32)
• Consequence: LOC101928923 XR_001744423.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689

Genes affected

LOC101928923 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0998 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928923	XR_001744423.2	n.406-17820A>C		intron_variant, non_coding_transcript_variant
LOC105378072	XR_001744424.2	n.80-20660T>G		intron_variant, non_coding_transcript_variant
LOC105378072	XR_007059824.1	n.80-20660T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0659 AC: 10018 AN: 152104 Hom.: 493 Cov.: 32

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0774

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.0580

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0658 AC: 10019 AN: 152222 Hom.: 493 Cov.: 32 AF XY: 0.0623 AC XY: 4634 AN XY: 74436

Gnomad4 AFR AF: 0.0191

Gnomad4 AMR AF: 0.0773

Gnomad4 ASJ AF: 0.0430

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0172

Gnomad4 FIN AF: 0.0580

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0908 Hom.: 885

Bravo AF: 0.0657

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11759141; hg19: chr6-156171848;