6-1514564-C-T

Variant summary

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

The ENST00000404600.2(ENSG00000218027):n.726G>A 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 0.398 in 1,528,490 control chromosomes in the GnomAD database, including 125,386 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 0.43 (15027 hom., cov: 33)
  • Exomes 𝑓: 0.39 (110359 hom.)
• Consequence: ENST00000404600.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723944	XR_427861.4	n.235-12001G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000404600.2	n.726G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65949 AN: 151902 Hom.: 14996 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.431

GnomAD4 exome AF: 0.394 AC: 542337 AN: 1376470 Hom.: 110359 Cov.: 30 AF XY: 0.397 AC XY: 270299 AN XY: 680880

Gnomad4 AFR exome AF: 0.541

Gnomad4 AMR exome AF: 0.297

Gnomad4 ASJ exome AF: 0.423

Gnomad4 EAS exome AF: 0.688

Gnomad4 SAS exome AF: 0.494

Gnomad4 FIN exome AF: 0.415

Gnomad4 NFE exome AF: 0.372

Gnomad4 OTH exome AF: 0.420

GnomAD4 genome AF: 0.434 AC: 66036 AN: 152020 Hom.: 15027 Cov.: 33 AF XY: 0.438 AC XY: 32566 AN XY: 74288

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.433

Alfa AF: 0.399 Hom.: 8281

Bravo AF: 0.435

Asia WGS AF: 0.563 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	8.4
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: rs9328058; hg19: chr6-1514799;