rs7584099

Variant names:

• chr2-147720767-A-G
• rs7584099
• ENST00000833959.1:n.126+16860T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-147720767-A-G
• chr2-147720767-A-T

Variant summary

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

The ENST00000833959.1(ENSG00000308424):​n.126+16860T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,990 control chromosomes in the GnomAD database, including 14,249 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 0.42 (14249 hom., cov: 32)
• Consequence: ENSG00000308424 ENST00000833959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 12 publications found

Genes affected

ENSG00000308424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.545 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
ENSG00000308424	ENST00000833959.1	n.126+16860T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63845 AN: 151872 Hom.: 14230 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.420 AC: 63905 AN: 151990 Hom.: 14249 Cov.: 32 AF XY: 0.431 AC XY: 31991 AN XY: 74286

African (AFR) AF: 0.275 AC: 11427 AN: 41486

American (AMR) AF: 0.555 AC: 8471 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3464

East Asian (EAS) AF: 0.508 AC: 2616 AN: 5154

South Asian (SAS) AF: 0.551 AC: 2652 AN: 4812

European-Finnish (FIN) AF: 0.517 AC: 5448 AN: 10540

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30789 AN: 67956

Other (OTH) AF: 0.417 AC: 879 AN: 2108

Alfa AF: 0.435 Hom.: 35175

Bravo AF: 0.414

Asia WGS AF: 0.554 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7584099; hg19: chr2-148478336;