rs72691625

Variant names:

• chr8-143212799-G-A
• rs72691625

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.151 in 152,260 control chromosomes in the GnomAD database, including 2,090 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency: Genomes: 𝑓 0.15 (2090 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 8-143212799-G-A is Benign according to our data. Variant chr8-143212799-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 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: 0.151 AC: 22954 AN: 152142 Hom.: 2092 Cov.: 33

Gnomad AFR AF: 0.0496

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.151 AC: 22949 AN: 152260 Hom.: 2090 Cov.: 33 AF XY: 0.154 AC XY: 11459 AN XY: 74432

Gnomad4 AFR AF: 0.0494

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.145

Alfa AF: 0.174 Hom.: 530

Bravo AF: 0.142

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72691625; hg19: chr8-144294674;