rs310272

chr8-23785976-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000523874.1(ENSG00000253471):n.76-2517C>G variant causes a intron, non coding transcript 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: ENST00000523874.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107986930	XR_001745842.2	n.1313-2517C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523874.1	n.76-2517C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.392

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs310272; hg19: chr8-23643489;