rs2616521

Variant names:

• chr3-5013893-T-C
• rs2616521
• ENST00000814585.1:n.351-1879A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-5013893-T-C
• chr3-5013893-T-G

Variant summary

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

The ENST00000814585.1(ENSG00000305983):​n.351-1879A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 151,994 control chromosomes in the GnomAD database, including 58,242 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 0.87 (58242 hom., cov: 31)
• Consequence: ENSG00000305983 ENST00000814585.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 2 publications found

Genes affected

ENSG00000305983 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305983	ENST00000814585.1	n.351-1879A>G		intron_variant	Intron 2 of 4
ENSG00000305983	ENST00000814586.1	n.124-1879A>G		intron_variant	Intron 1 of 3
ENSG00000305983	ENST00000814587.1	n.127-1879A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132622 AN: 151876 Hom.: 58199 Cov.: 31

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.873 AC: 132721 AN: 151994 Hom.: 58242 Cov.: 31 AF XY: 0.869 AC XY: 64576 AN XY: 74280

African (AFR) AF: 0.787 AC: 32573 AN: 41386

American (AMR) AF: 0.854 AC: 13045 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3217 AN: 3470

East Asian (EAS) AF: 0.833 AC: 4303 AN: 5168

South Asian (SAS) AF: 0.820 AC: 3955 AN: 4822

European-Finnish (FIN) AF: 0.884 AC: 9323 AN: 10550

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63287 AN: 68018

Other (OTH) AF: 0.893 AC: 1881 AN: 2106

Alfa AF: 0.907 Hom.: 29984

Bravo AF: 0.866

Asia WGS AF: 0.800 AC: 2783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.40
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs2616521; hg19: chr3-5055578;