rs973582

Variant names:

• chr8-14051673-G-A
• rs973582

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

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

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

African (AFR) AF: 0.155 AC: 6418 AN: 41468

American (AMR) AF: 0.283 AC: 4316 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3470

East Asian (EAS) AF: 0.488 AC: 2500 AN: 5126

South Asian (SAS) AF: 0.398 AC: 1915 AN: 4816

European-Finnish (FIN) AF: 0.225 AC: 2383 AN: 10570

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22776 AN: 67940

Other (OTH) AF: 0.277 AC: 586 AN: 2112

Alfa AF: 0.300 Hom.: 1254

Bravo AF: 0.278

Asia WGS AF: 0.428 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.60
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs973582; hg19: chr8-13909182;