rs973582

Variant names:

• chr8-14051673-G-A
• rs973582

Variant summary

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

The variant allele was found at a frequency of 0.28 in 151,946 control chromosomes in the GnomAD database, including 6,565 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 0.28 (6565 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) 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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42502 AN: 151826 Hom.: 6567 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.280 AC: 42512 AN: 151946 Hom.: 6565 Cov.: 31 AF XY: 0.278 AC XY: 20604 AN XY: 74220

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.277

Alfa AF: 0.304 Hom.: 1249

Bravo AF: 0.278

Asia WGS AF: 0.428 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs973582; hg19: chr8-13909182;