6-35765922-A-G

Position:

• chr6-35765922-A-G

Variant summary

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

The ENST00000403727.1(ENSG00000220734):​n.15A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 428,856 control chromosomes in the GnomAD database, including 106,686 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 0.69 (37105 hom., cov: 33)
  • Exomes 𝑓: 0.70 (69581 hom.)
• Consequence: ENSG00000220734 ENST00000403727.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

ENSG00000220734 (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 (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.35765922A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000220734	ENST00000403727.1	n.15A>G		non_coding_transcript_exon_variant	1/2	6

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104108 AN: 152000 Hom.: 37045 Cov.: 33

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.718

GnomAD4 exome AF: 0.704 AC: 194746 AN: 276738 Hom.: 69581 Cov.: 0 AF XY: 0.710 AC XY: 106607 AN XY: 150224

Gnomad4 AFR exome AF: 0.925

Gnomad4 AMR exome AF: 0.678

Gnomad4 ASJ exome AF: 0.846

Gnomad4 EAS exome AF: 0.562

Gnomad4 SAS exome AF: 0.770

Gnomad4 FIN exome AF: 0.611

Gnomad4 NFE exome AF: 0.693

Gnomad4 OTH exome AF: 0.733

GnomAD4 genome AF: 0.685 AC: 104222 AN: 152118 Hom.: 37105 Cov.: 33 AF XY: 0.682 AC XY: 50697 AN XY: 74338

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.720

Alfa AF: 0.503 Hom.: 1310

Bravo AF: 0.693

Asia WGS AF: 0.647 AC: 2249 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	5.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2817054; hg19: chr6-35733699;