rs310272

Variant names:

• chr8-23785976-C-G
• rs310272
• ENST00000523874.1:n.76-2517C>G

Variant summary

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

The ENST00000523874.1(ENSG00000253471):​n.76-2517C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,046 control chromosomes in the GnomAD database, including 11,943 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 0.39 (11943 hom., cov: 32)
• Consequence: ENSG00000253471 ENST00000523874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 2 publications found

Genes affected

ENSG00000253471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986930	XR_001745842.2	n.1313-2517C>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253471	ENST00000523874.1	n.76-2517C>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59569 AN: 151928 Hom.: 11920 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.392 AC: 59654 AN: 152046 Hom.: 11943 Cov.: 32 AF XY: 0.391 AC XY: 29081 AN XY: 74354

African (AFR) AF: 0.477 AC: 19804 AN: 41478

American (AMR) AF: 0.453 AC: 6912 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1293 AN: 5166

South Asian (SAS) AF: 0.364 AC: 1759 AN: 4826

European-Finnish (FIN) AF: 0.356 AC: 3769 AN: 10578

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24140 AN: 67944

Other (OTH) AF: 0.392 AC: 827 AN: 2112

Alfa AF: 0.378 Hom.: 1372

Bravo AF: 0.403

Asia WGS AF: 0.358 AC: 1246 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.72
DANN	Benign	0.41
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs310272; hg19: chr8-23643489;