rs9878275

Variant names:

• chr3-45314547-A-C
• rs9878275
• ENST00000756647.1:n.34+2260A>C

Variant summary

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

The ENST00000756647.1(ENSG00000298579):​n.34+2260A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 152,268 control chromosomes in the GnomAD database, including 696 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 0.056 (696 hom., cov: 32)
• Consequence: ENSG00000298579 ENST00000756647.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 1 publications found

Genes affected

ENSG00000298579 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377061	XR_001740678.1	n.980+4396A>C		intron_variant	Intron 2 of 2
LOC105377061	XR_001740679.1	n.980+4396A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298579	ENST00000756647.1	n.34+2260A>C		intron_variant	Intron 1 of 1
ENSG00000298579	ENST00000756648.1	n.46+2260A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0559 AC: 8507 AN: 152150 Hom.: 689 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0242

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00237

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0562 AC: 8559 AN: 152268 Hom.: 696 Cov.: 32 AF XY: 0.0559 AC XY: 4159 AN XY: 74466

African (AFR) AF: 0.179 AC: 7429 AN: 41524

American (AMR) AF: 0.0235 AC: 360 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3468

East Asian (EAS) AF: 0.0241 AC: 125 AN: 5188

South Asian (SAS) AF: 0.0783 AC: 378 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00237 AC: 161 AN: 68022

Other (OTH) AF: 0.0426 AC: 90 AN: 2114

Alfa AF: 0.0417 Hom.: 66

Bravo AF: 0.0625

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.44
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs9878275; hg19: chr3-45356039;