rs9379851

chr6-26354552-A-C

Variant summary

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

The ENST00000707189.1(ENSG00000291336):n.1000-198635A>C 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 0.0769 in 152,256 control chromosomes in the GnomAD database, including 567 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 0.077 (567 hom., cov: 32)
• Consequence: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000707189.1	n.1000-198635A>C		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-178153A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11718 AN: 152138 Hom.: 568 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0701

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

GnomAD4 genome AF: 0.0769 AC: 11709 AN: 152256 Hom.: 567 Cov.: 32 AF XY: 0.0737 AC XY: 5489 AN XY: 74440

Gnomad4 AFR AF: 0.0344

Gnomad4 AMR AF: 0.0408

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.0866

Gnomad4 SAS AF: 0.0972

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0703

Alfa AF: 0.103 Hom.: 315

Bravo AF: 0.0721

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.75
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9379851; hg19: chr6-26354780;