6-108545828-C-A

Position:

• chr6-108545828-C-A

Variant summary

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

The ENST00000659932.1(ENSG00000287044):​n.123+12336G>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 0.46 in 152,046 control chromosomes in the GnomAD database, including 17,043 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 0.46 (17043 hom., cov: 33)
• Consequence: ENST00000659932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000659932.1	n.123+12336G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69879 AN: 151928 Hom.: 17038 Cov.: 33

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.460 AC: 69927 AN: 152046 Hom.: 17043 Cov.: 33 AF XY: 0.460 AC XY: 34159 AN XY: 74308

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.455

Alfa AF: 0.394 Hom.: 24638

Bravo AF: 0.459

Asia WGS AF: 0.473 AC: 1643 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	2.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6911407; hg19: chr6-108867031; COSMIC: COSV60264957;