rs72691625

Variant names:

• chr8-143212799-G-A
• rs72691625

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 0.151 in 152,260 control chromosomes in the GnomAD database, including 2,090 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 0.15 (2090 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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

African (AFR) AF: 0.0494 AC: 2055 AN: 41574

American (AMR) AF: 0.184 AC: 2811 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3472

East Asian (EAS) AF: 0.185 AC: 957 AN: 5178

South Asian (SAS) AF: 0.157 AC: 759 AN: 4830

European-Finnish (FIN) AF: 0.244 AC: 2586 AN: 10602

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12666 AN: 67990

Other (OTH) AF: 0.145 AC: 306 AN: 2112

Alfa AF: 0.171 Hom.: 531

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
PhyloP100		-0.30
PromoterAI		-0.027	Neutral

Splicing

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

Other links and lift over

dbSNP: rs72691625; hg19: chr8-144294674;