rs41519045

chr6-31371309-G-Achr6-31371309-G-C

Variant summary

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

The ENST00000649421.1(ENSG00000285647):n.275-3574G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 150,322 control chromosomes in the GnomAD database, including 54,127 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 0.85 (54127 hom., cov: 30)
• Consequence: ENST00000649421.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.907 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
	ENST00000649421.1	n.275-3574G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.846 AC: 127068 AN: 150214 Hom.: 54079 Cov.: 30

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.929

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.846 AC: 127168 AN: 150322 Hom.: 54127 Cov.: 30 AF XY: 0.849 AC XY: 62217 AN XY: 73270

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.926

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.879

Alfa AF: 0.828 Hom.: 8101

Bravo AF: 0.846

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.2
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41519045; hg19: chr6-31339086;