rs72691625

Positions:

• chr8-143212799-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;