rs5007872

Variant names:

• chr8-72534635-G-A
• rs5007872

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 0.727 in 152,146 control chromosomes in the GnomAD database, including 40,231 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 0.73 (40231 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.774 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: 0.727 AC: 110449 AN: 152028 Hom.: 40191 Cov.: 33

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.727 AC: 110542 AN: 152146 Hom.: 40231 Cov.: 33 AF XY: 0.728 AC XY: 54138 AN XY: 74380

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.723

Alfa AF: 0.730 Hom.: 5042

Bravo AF: 0.731

Asia WGS AF: 0.710 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5007872; hg19: chr8-73446870;