rs10515041

Variant names:

• chr5-67267231-G-A
• rs10515041
• ENST00000824927.1:n.257+22569G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-67267231-G-A
• chr5-67267231-G-T

Variant summary

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

The ENST00000824927.1(ENSG00000307284):​n.257+22569G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 152,194 control chromosomes in the GnomAD database, including 837 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 0.062 (837 hom., cov: 32)
• Consequence: ENSG00000307284 ENST00000824927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 2 publications found

Genes affected

ENSG00000307284 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.198 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
ENSG00000307284	ENST00000824927.1	n.257+22569G>A		intron_variant	Intron 2 of 2
ENSG00000307284	ENST00000824928.1	n.211+22569G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0618 AC: 9392 AN: 152076 Hom.: 832 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00567

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0619 AC: 9426 AN: 152194 Hom.: 837 Cov.: 32 AF XY: 0.0601 AC XY: 4474 AN XY: 74414

African (AFR) AF: 0.202 AC: 8365 AN: 41472

American (AMR) AF: 0.0261 AC: 399 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0114 AC: 55 AN: 4824

European-Finnish (FIN) AF: 0.00179 AC: 19 AN: 10600

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00567 AC: 386 AN: 68022

Other (OTH) AF: 0.0512 AC: 108 AN: 2110

Alfa AF: 0.0230 Hom.: 57

Bravo AF: 0.0699

Asia WGS AF: 0.0180 AC: 63 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	0.85
DANN	Benign	0.54
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs10515041; hg19: chr5-66563059;