6-26455277-G-C

Variant summary

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

The ENST00000707189.1(ENSG00000291336):n.1000-97910G>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 0.65 in 152,088 control chromosomes in the GnomAD database, including 35,323 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 0.65 (35323 hom., cov: 32)
• Consequence: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 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.1000-97910G>C		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-77428G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98791 AN: 151970 Hom.: 35319 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.650 AC: 98816 AN: 152088 Hom.: 35323 Cov.: 32 AF XY: 0.652 AC XY: 48511 AN XY: 74362

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.657

Alfa AF: 0.714 Hom.: 5130

Bravo AF: 0.624

Asia WGS AF: 0.736 AC: 2563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.32
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6456723; hg19: chr6-26455505;