6-26148772-T-C

Variant names:

• chr6-26148772-T-C
• rs16891359
• ENST00000707189.1:n.999+24601T>C

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+24601T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0859 in 151,576 control chromosomes in the GnomAD database, including 1,709 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 0.086 (1709 hom., cov: 31)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 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
ENSG00000291336	ENST00000707189.1	n.999+24601T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 12990 AN: 151456 Hom.: 1697 Cov.: 31

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0384

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.0613

Gnomad NFE AF: 0.0480

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0859 AC: 13018 AN: 151576 Hom.: 1709 Cov.: 31 AF XY: 0.0997 AC XY: 7386 AN XY: 74112

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.0384

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.0480

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.0583 Hom.: 269

Bravo AF: 0.0811

Asia WGS AF: 0.382 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16891359; hg19: chr6-26149000;