rs2294478

Variant names:

• chr6-33131189-C-A
• rs2294478
• ENST00000782892.1:n.430-9932C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-33131189-C-A
• chr6-33131189-C-G

Variant summary

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

The NR_190905.1(LOC105375021):​n.638+8G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,098 control chromosomes in the GnomAD database, including 17,024 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 0.46 (17009 hom., cov: 32)
  • Exomes 𝑓: 0.42 (15 hom.)
• Consequence: LOC105375021 NR_190905.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 30 publications found

Genes affected

ENSG00000291111 (HGNC:):

ENSG00000301948 (HGNC:59163):

HLA-DPA3 (HGNC:19393): (major histocompatibility complex, class II, DP alpha 3 (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_190905.1. 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
	LOC105375021	NR_190905.1		n.638+8G>T		splice_region intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291111	ENST00000782892.1		n.430-9932C>A		intron	N/A
	ENSG00000291111	ENST00000782893.1		n.404-9932C>A		intron	N/A
	ENSG00000291111	ENST00000782894.1		n.229-56C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69359 AN: 151836 Hom.: 16996 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.493

GnomAD4 exome AF: 0.424 AC: 61 AN: 144 Hom.: 15 Cov.: 0 AF XY: 0.429 AC XY: 42 AN XY: 98

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.625 AC: 5 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.500 AC: 2 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.667 AC: 8 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.440 AC: 44 AN: 100

Other (OTH) AF: 0.143 AC: 2 AN: 14

GnomAD4 genome AF: 0.457 AC: 69403 AN: 151954 Hom.: 17009 Cov.: 32 AF XY: 0.463 AC XY: 34407 AN XY: 74280

African (AFR) AF: 0.296 AC: 12259 AN: 41422

American (AMR) AF: 0.572 AC: 8739 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2229 AN: 3470

East Asian (EAS) AF: 0.772 AC: 3968 AN: 5140

South Asian (SAS) AF: 0.590 AC: 2838 AN: 4810

European-Finnish (FIN) AF: 0.480 AC: 5072 AN: 10556

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32613 AN: 67968

Other (OTH) AF: 0.497 AC: 1048 AN: 2110

Alfa AF: 0.477 Hom.: 51731

Bravo AF: 0.459

Asia WGS AF: 0.616 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.77
PhyloP100		-0.43

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: rs2294478;

hg19: chr6-33098966;