10-87982049-G-A

Variant names:

• chr10-87982049-G-A
• rs809367
• ENST00000752269.1:n.64+1929G>A

Variant summary

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

The ENST00000752269.1(ENSG00000297977):​n.64+1929G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,668 control chromosomes in the GnomAD database, including 1,218 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 0.12 (1218 hom., cov: 31)
• Consequence: ENSG00000297977 ENST00000752269.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 3 publications found

Genes affected

ENSG00000297977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752269.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297977	ENST00000752269.1		n.64+1929G>A		intron	N/A
	ENSG00000297977	ENST00000752273.1		n.111+1242G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18207 AN: 151550 Hom.: 1214 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0639

Gnomad FIN AF: 0.0799

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0961

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.120 AC: 18225 AN: 151668 Hom.: 1218 Cov.: 31 AF XY: 0.118 AC XY: 8720 AN XY: 74118

African (AFR) AF: 0.152 AC: 6283 AN: 41312

American (AMR) AF: 0.175 AC: 2663 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 501 AN: 3470

East Asian (EAS) AF: 0.133 AC: 683 AN: 5124

South Asian (SAS) AF: 0.0639 AC: 306 AN: 4786

European-Finnish (FIN) AF: 0.0799 AC: 842 AN: 10542

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0961 AC: 6522 AN: 67872

Other (OTH) AF: 0.129 AC: 271 AN: 2104

Alfa AF: 0.112 Hom.: 1274

Bravo AF: 0.130

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.41
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs809367; hg19: chr10-89741806;