rs10804287

Variant names:

• chr2-220281744-G-A
• rs10804287
• ENST00000432993.1:n.307-40357G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-220281744-G-A
• chr2-220281744-G-T

Variant summary

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

The ENST00000432993.1(ENSG00000288902):​n.307-40357G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,110 control chromosomes in the GnomAD database, including 3,784 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 0.21 (3784 hom., cov: 32)
• Consequence: ENSG00000288902 ENST00000432993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.986
• Publications: 4 publications found

Genes affected

ENSG00000288902 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373893	XR_001739889.2	n.274-40357G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288902	ENST00000432993.1	n.307-40357G>A		intron_variant	Intron 1 of 3	3
ENSG00000288902	ENST00000830324.1	n.694-40357G>A		intron_variant	Intron 4 of 5
ENSG00000288902	ENST00000830325.1	n.303-40357G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32375 AN: 151992 Hom.: 3781 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.213 AC: 32394 AN: 152110 Hom.: 3784 Cov.: 32 AF XY: 0.216 AC XY: 16079 AN XY: 74360

African (AFR) AF: 0.124 AC: 5152 AN: 41484

American (AMR) AF: 0.248 AC: 3787 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3468

East Asian (EAS) AF: 0.366 AC: 1890 AN: 5166

South Asian (SAS) AF: 0.304 AC: 1468 AN: 4824

European-Finnish (FIN) AF: 0.213 AC: 2252 AN: 10570

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16242 AN: 68012

Other (OTH) AF: 0.234 AC: 493 AN: 2110

Alfa AF: 0.229 Hom.: 7162

Bravo AF: 0.207

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.2
DANN	Benign	0.64
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs10804287; hg19: chr2-221146465;