rs2309717

Variant names:

• chr4-28248616-C-A
• rs2309717
• ENST00000668598.1:n.92+22556C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-28248616-C-A
• chr4-28248616-C-T

Variant summary

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

The ENST00000668598.1(ENSG00000286321):​n.92+22556C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,948 control chromosomes in the GnomAD database, including 3,126 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 0.19 (3126 hom., cov: 31)
• Consequence: ENSG00000286321 ENST00000668598.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.761
• Publications: 3 publications found

Genes affected

ENSG00000286321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374557	NR_188396.1	n.287+33468C>A		intron_variant	Intron 2 of 4
LOC105374557	NR_188397.1	n.287+33468C>A		intron_variant	Intron 2 of 3
LOC105374557	NR_188398.1	n.287+33468C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286321	ENST00000668598.1	n.92+22556C>A		intron_variant	Intron 1 of 1
ENSG00000286321	ENST00000742923.1	n.222+33468C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29520 AN: 151830 Hom.: 3122 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.195 AC: 29554 AN: 151948 Hom.: 3126 Cov.: 31 AF XY: 0.195 AC XY: 14464 AN XY: 74282

African (AFR) AF: 0.269 AC: 11153 AN: 41422

American (AMR) AF: 0.222 AC: 3377 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3468

East Asian (EAS) AF: 0.289 AC: 1487 AN: 5154

South Asian (SAS) AF: 0.206 AC: 991 AN: 4820

European-Finnish (FIN) AF: 0.141 AC: 1489 AN: 10570

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9886 AN: 67962

Other (OTH) AF: 0.193 AC: 406 AN: 2104

Alfa AF: 0.161 Hom.: 3522

Bravo AF: 0.204

Asia WGS AF: 0.208 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82
DANN	Benign	0.72
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2309717; hg19: chr4-28250238;