rs1935924

Variant names:

• chr10-52828330-G-A
• rs1935924
• ENST00000816733.1:n.692+17633G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-52828330-G-A
• chr10-52828330-G-C
• chr10-52828330-G-T

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.692+17633G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 128,098 control chromosomes in the GnomAD database, including 17,331 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 0.52 (17331 hom., cov: 24)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 5 publications found

Genes affected

ENSG00000306279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 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
ENSG00000306279	ENST00000816733.1	n.692+17633G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.523 AC: 66933 AN: 128028 Hom.: 17326 Cov.: 24

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.569

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.523 AC: 66942 AN: 128098 Hom.: 17331 Cov.: 24 AF XY: 0.522 AC XY: 32447 AN XY: 62108

African (AFR) AF: 0.289 AC: 8135 AN: 28124

American (AMR) AF: 0.443 AC: 5656 AN: 12780

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 1984 AN: 3200

East Asian (EAS) AF: 0.587 AC: 2611 AN: 4450

South Asian (SAS) AF: 0.580 AC: 2496 AN: 4302

European-Finnish (FIN) AF: 0.644 AC: 5932 AN: 9216

Middle Eastern (MID) AF: 0.565 AC: 139 AN: 246

European-Non Finnish (NFE) AF: 0.609 AC: 38480 AN: 63154

Other (OTH) AF: 0.542 AC: 960 AN: 1770

Alfa AF: 0.530 Hom.: 84118

Bravo AF: 0.423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.36
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1935924; hg19: chr10-54588090;