6-31371309-G-A

Variant names:

• chr6-31371309-G-A
• rs41519045
• ENST00000649421.2:n.275-3574G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649421.2(ENSG00000285647):​n.275-3574G>A variant causes a intron 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: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 5 publications found

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285647	ENST00000649421.2	n.275-3574G>A		intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1	n.327-10671G>A		intron_variant	Intron 1 of 1
ENSG00000285647	ENST00000755530.1	n.203-3574G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.836 AC: 34549 AN: 41310

American (AMR) AF: 0.888 AC: 13084 AN: 14738

Ashkenazi Jewish (ASJ) AF: 0.926 AC: 3203 AN: 3460

East Asian (EAS) AF: 0.929 AC: 4707 AN: 5068

South Asian (SAS) AF: 0.929 AC: 4255 AN: 4580

European-Finnish (FIN) AF: 0.833 AC: 8512 AN: 10216

Middle Eastern (MID) AF: 0.924 AC: 268 AN: 290

European-Non Finnish (NFE) AF: 0.826 AC: 55923 AN: 67670

Other (OTH) AF: 0.879 AC: 1826 AN: 2078

Alfa AF: 0.829 Hom.: 9043

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
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs41519045; hg19: chr6-31339086;