rs1576313

Variant names:

• chr10-18846766-G-A
• rs1576313
• ENST00000723466.1:n.344+10534G>A

Variant summary

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

The ENST00000723466.1(ENSG00000234244):​n.344+10534G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,954 control chromosomes in the GnomAD database, including 2,920 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 0.19 (2920 hom., cov: 33)
• Consequence: ENSG00000234244 ENST00000723466.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 1 publications found

Genes affected

ENSG00000234244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 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
ENSG00000234244	ENST00000723466.1	n.344+10534G>A		intron_variant	Intron 5 of 7
ENSG00000234244	ENST00000723467.1	n.305+10534G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28303 AN: 151836 Hom.: 2920 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.186 AC: 28318 AN: 151954 Hom.: 2920 Cov.: 33 AF XY: 0.183 AC XY: 13582 AN XY: 74270

African (AFR) AF: 0.259 AC: 10738 AN: 41390

American (AMR) AF: 0.231 AC: 3540 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3468

East Asian (EAS) AF: 0.232 AC: 1201 AN: 5172

South Asian (SAS) AF: 0.140 AC: 675 AN: 4816

European-Finnish (FIN) AF: 0.0951 AC: 1005 AN: 10566

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.149 AC: 10099 AN: 67942

Other (OTH) AF: 0.190 AC: 400 AN: 2102

Alfa AF: 0.158 Hom.: 1047

Bravo AF: 0.208

Asia WGS AF: 0.195 AC: 674 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.76
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs1576313; hg19: chr10-19135695;