rs438465

chr6-169420286-T-Cchr6-169420286-T-G

Variant summary

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

The ENST00000649318.1(ENSG00000285887):n.2876A>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 0.819 in 152,004 control chromosomes in the GnomAD database, including 51,871 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 (51871 hom., cov: 30)
• Consequence: ENST00000649318.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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
	ENST00000649318.1	n.2876A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124388 AN: 151884 Hom.: 51825 Cov.: 30

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.819 AC: 124488 AN: 152004 Hom.: 51871 Cov.: 30 AF XY: 0.811 AC XY: 60240 AN XY: 74268

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.823

Alfa AF: 0.825 Hom.: 19801

Bravo AF: 0.815

Asia WGS AF: 0.647 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.69
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs438465; hg19: chr6-169820381;