rs224309

Variant names:

• chr10-62848544-A-C
• rs224309
• ENST00000493899.2:n.542-32575T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-62848544-A-C
• chr10-62848544-A-G
• chr10-62848544-A-T

Variant summary

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

The ENST00000493899.2(ENSG00000289487):​n.542-32575T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,066 control chromosomes in the GnomAD database, including 13,664 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 (13664 hom., cov: 32)
• Consequence: ENSG00000289487 ENST00000493899.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

Genes affected

ENSG00000289487 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 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
ENSG00000289487	ENST00000493899.2	n.542-32575T>G		intron_variant	Intron 6 of 7	5

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63928 AN: 151948 Hom.: 13661 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.421 AC: 63944 AN: 152066 Hom.: 13664 Cov.: 32 AF XY: 0.416 AC XY: 30928 AN XY: 74342

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.413

Alfa AF: 0.400 Hom.: 1525

Bravo AF: 0.418

Asia WGS AF: 0.377 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs224309; hg19: chr10-64608304;