rs2215921

Variant names:

• chr16-9603476-G-A
• rs2215921
• ENST00000634367.2:n.575-11045G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-9603476-G-A
• chr16-9603476-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634367.2(ENSG00000283003):​n.575-11045G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,016 control chromosomes in the GnomAD database, including 9,086 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 0.33 (9086 hom., cov: 32)
• Consequence: ENSG00000283003 ENST00000634367.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

ENSG00000283003 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 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
ENSG00000283003	ENST00000634367.2	n.575-11045G>A		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49822 AN: 151898 Hom.: 9092 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.328 AC: 49824 AN: 152016 Hom.: 9086 Cov.: 32 AF XY: 0.326 AC XY: 24231 AN XY: 74298

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.351

Alfa AF: 0.381 Hom.: 22869

Bravo AF: 0.318

Asia WGS AF: 0.423 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.4
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215921; hg19: chr16-9697333;