rs2596438

chr6-31372094-G-Achr6-31372094-G-Cchr6-31372094-G-T

Variant summary

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

The ENST00000649421.1(ENSG00000285647):n.275-2789G>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 0.848 in 151,244 control chromosomes in the GnomAD database, including 54,811 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 (54811 hom., cov: 33)
• Consequence: ENST00000649421.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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.275-2789G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128188 AN: 151130 Hom.: 54759 Cov.: 33

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.848 AC: 128295 AN: 151244 Hom.: 54811 Cov.: 33 AF XY: 0.852 AC XY: 62854 AN XY: 73806

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.931

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.882

Alfa AF: 0.787 Hom.: 3376

Bravo AF: 0.851

Asia WGS AF: 0.925 AC: 3149 AN: 3404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.8
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2596438; hg19: chr6-31339871;