rs2244020

Variant names:

• chr6-31379674-A-G
• rs2244020
• ENST00000755446.1:n.327-2306A>G

Variant summary

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

The ENST00000755446.1(ENSG00000298426):​n.327-2306A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.54 (17829 hom., cov: 18)
• Consequence: ENSG00000298426 ENST00000755446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 42 publications found

Genes affected

ENSG00000298426 (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 (AFR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298426	ENST00000755446.1		n.327-2306A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.543 AC: 64976 AN: 119748 Hom.: 17835 Cov.: 18

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.681

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.542 AC: 64965 AN: 119754 Hom.: 17829 Cov.: 18 AF XY: 0.546 AC XY: 31223 AN XY: 57180

African (AFR) AF: 0.707 AC: 24366 AN: 34460

American (AMR) AF: 0.614 AC: 7330 AN: 11938

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2366 AN: 3252

East Asian (EAS) AF: 0.559 AC: 2439 AN: 4366

South Asian (SAS) AF: 0.541 AC: 2116 AN: 3910

European-Finnish (FIN) AF: 0.391 AC: 2216 AN: 5664

Middle Eastern (MID) AF: 0.675 AC: 162 AN: 240

European-Non Finnish (NFE) AF: 0.422 AC: 22577 AN: 53530

Other (OTH) AF: 0.598 AC: 994 AN: 1662

Alfa AF: 0.424 Hom.: 33604

Asia WGS AF: 0.386 AC: 1130 AN: 2932

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	9.3
DANN	Benign	0.48
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2244020; hg19: chr6-31347451;