rs2394990

Variant names:

• chr6-31372782-C-A
• rs2394990
• ENST00000649421.2:n.275-2101C>A

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.275-2101C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 150,458 control chromosomes in the GnomAD database, including 25,342 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 0.57 (25342 hom., cov: 30)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 12 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649421.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285647	ENST00000649421.2		n.275-2101C>A		intron	N/A
	ENSG00000298426	ENST00000755446.1		n.327-9198C>A		intron	N/A
	ENSG00000285647	ENST00000755530.1		n.203-2101C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.569 AC: 85472 AN: 150344 Hom.: 25324 Cov.: 30

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.600

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.568 AC: 85525 AN: 150458 Hom.: 25342 Cov.: 30 AF XY: 0.566 AC XY: 41462 AN XY: 73280

African (AFR) AF: 0.501 AC: 20656 AN: 41264

American (AMR) AF: 0.515 AC: 7635 AN: 14830

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1430 AN: 3460

East Asian (EAS) AF: 0.717 AC: 3617 AN: 5046

South Asian (SAS) AF: 0.658 AC: 2998 AN: 4558

European-Finnish (FIN) AF: 0.509 AC: 5228 AN: 10280

Middle Eastern (MID) AF: 0.594 AC: 171 AN: 288

European-Non Finnish (NFE) AF: 0.620 AC: 42023 AN: 67726

Other (OTH) AF: 0.590 AC: 1238 AN: 2100

Alfa AF: 0.600 Hom.: 22351

Bravo AF: 0.564

Asia WGS AF: 0.641 AC: 2182 AN: 3404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.16
PhyloP100		-0.58

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2394990;

hg19: chr6-31340559;