6-134098874-G-A

Position:

• chr6-134098874-G-A

Variant summary

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

The ENST00000663785.1(ENSG00000287413):​n.350+12863G>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 0.375 in 151,946 control chromosomes in the GnomAD database, including 11,221 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 0.37 (11221 hom., cov: 31)
• Consequence: ENST00000663785.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901404	XR_007059774.1	n.2284+12863G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663785.1	n.350+12863G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56872 AN: 151826 Hom.: 11199 Cov.: 31

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.375 AC: 56928 AN: 151946 Hom.: 11221 Cov.: 31 AF XY: 0.373 AC XY: 27722 AN XY: 74274

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.354

Alfa AF: 0.361 Hom.: 20842

Bravo AF: 0.362

Asia WGS AF: 0.234 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6569926; hg19: chr6-134420012; COSMIC: COSV69427304;