6-129895365-A-G

Position:

• chr6-129895365-A-G

Variant summary

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

The XR_942986.3(LOC105377999):​n.355+7292A>G 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 0.526 in 151,868 control chromosomes in the GnomAD database, including 21,241 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 0.53 (21241 hom., cov: 30)
• Consequence: LOC105377999 XR_942986.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.54

Genes affected

LOC105377999 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377999	XR_942986.3	n.355+7292A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79816 AN: 151750 Hom.: 21218 Cov.: 30

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.526 AC: 79883 AN: 151868 Hom.: 21241 Cov.: 30 AF XY: 0.527 AC XY: 39101 AN XY: 74224

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.504

Alfa AF: 0.534 Hom.: 31119

Bravo AF: 0.528

Asia WGS AF: 0.569 AC: 1979 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.081
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9375674; hg19: chr6-130216510;