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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432993.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288902	ENST00000432993.1	TSL:3	n.307-40357G>A		intron	N/A
	ENSG00000288902	ENST00000830324.1		n.694-40357G>A		intron	N/A
	ENSG00000288902	ENST00000830325.1		n.303-40357G>A		intron	N/A

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 v4.9

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;