6-29762865-A-G

Variant summary

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

The ENST00000648999.1(ENSG00000285761):n.1447A>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 0.816 in 152,208 control chromosomes in the GnomAD database, including 50,952 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 0.82 (50952 hom., cov: 33)
• Consequence: ENST00000648999.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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
	ENST00000648999.1	n.1447A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124042 AN: 152090 Hom.: 50891 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.816 AC: 124162 AN: 152208 Hom.: 50952 Cov.: 33 AF XY: 0.814 AC XY: 60559 AN XY: 74410

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.825

Alfa AF: 0.819 Hom.: 29210

Bravo AF: 0.827

Asia WGS AF: 0.939 AC: 3267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.8
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1633048; hg19: chr6-29730642;