rs6911407

Variant names:

• chr6-108545828-C-A
• rs6911407
• ENST00000659932.2:n.136+12336G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659932.2(ENSG00000287044):​n.136+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 ENST00000659932.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 10 publications found

Genes affected

ENSG00000287044 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000659932.2	n.136+12336G>T		intron_variant	Intron 1 of 3
ENSG00000287044	ENST00000784390.1	n.119+12336G>T		intron_variant	Intron 1 of 1
ENSG00000287044	ENST00000784391.1	n.126+12336G>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.631 AC: 26196 AN: 41484

American (AMR) AF: 0.393 AC: 6006 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1254 AN: 3472

East Asian (EAS) AF: 0.356 AC: 1836 AN: 5156

South Asian (SAS) AF: 0.541 AC: 2610 AN: 4820

European-Finnish (FIN) AF: 0.433 AC: 4573 AN: 10552

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.384 AC: 26103 AN: 67968

Other (OTH) AF: 0.455 AC: 959 AN: 2108

Alfa AF: 0.400 Hom.: 52827

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
PhyloP100		0.019

Splicing

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

Other links and lift over

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