6-100889735-A-G

Position:

• chr6-100889735-A-G

Variant summary

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

The ENST00000604292.1(ENSG00000270987):​n.133A>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 0.523 in 1,613,470 control chromosomes in the GnomAD database, including 224,165 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 0.51 (20476 hom., cov: 33)
  • Exomes 𝑓: 0.52 (203689 hom.)
• Consequence: ENST00000604292.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984041	XR_007059692.1	n.199-2263A>G		intron_variant, non_coding_transcript_variant
LOC107984041	XR_002956381.2	n.199-2263A>G		intron_variant, non_coding_transcript_variant
LOC107984041	XR_002956382.2	n.199-2263A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000604292.1	n.133A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78190 AN: 151880 Hom.: 20447 Cov.: 33

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 0.524 AC: 765918 AN: 1461472 Hom.: 203689 Cov.: 47 AF XY: 0.519 AC XY: 377643 AN XY: 727052

Gnomad4 AFR exome AF: 0.441

Gnomad4 AMR exome AF: 0.650

Gnomad4 ASJ exome AF: 0.529

Gnomad4 EAS exome AF: 0.780

Gnomad4 SAS exome AF: 0.387

Gnomad4 FIN exome AF: 0.509

Gnomad4 NFE exome AF: 0.524

Gnomad4 OTH exome AF: 0.523

GnomAD4 genome AF: 0.515 AC: 78265 AN: 151998 Hom.: 20476 Cov.: 33 AF XY: 0.514 AC XY: 38190 AN XY: 74324

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.536

Alfa AF: 0.511 Hom.: 3206

Bravo AF: 0.527

Asia WGS AF: 0.558 AC: 1937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9498419; hg19: chr6-101337611;