rs6911407

Variant names:

• chr6-108545828-C-A
• rs6911407
• ENST00000659932.1:n.123+12336G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-108545828-C-A
• chr6-108545828-C-T

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 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: ENSG00000287044 ENST00000659932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

ENSG00000287044 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287044	ENST00000659932.1	n.123+12336G>T		intron_variant	Intron 1 of 3

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;